DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=1.025e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_2L_t	0.007689

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	9.2533	0.0098

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2561 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	5878383	3R_5878383_SNP [dm3] 3R_10052661_SNP [dm6]	G	T	4.774e^-8	0.055	UPSTREAM Npc2e DOWNSTREAM CR44192 INTRON Fancl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	5878395	3R_5878395_SNP [dm3] 3R_10052673_SNP [dm6]	A	G	5.907e^-8	0.055	UPSTREAM Npc2e DOWNSTREAM CR44192 INTRON Fancl	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	5878522	3R_5878522_SNP [dm3] 3R_10052800_SNP [dm6]	T	C	3.547e^-7	0.197	NON_SYNONYMOUS_CODING Fancl UPSTREAM Npc2e DOWNSTREAM CR44192	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	21896719	3R_21896719_SNP [dm3] 3R_26070997_SNP [dm6]	C	T	4.213e^-7	0.197	EXON CR44950
3L	9715763	3L_9715763_SNP [dm3] 3L_9722663_SNP [dm6]	C	T	5.462e^-7	0.205	NON_SYNONYMOUS_CODING nbs UPSTREAM defl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	18159767	X_18159767_SNP [dm3] X_18265734_SNP [dm6]	G	A	1.927e^-6	0.516	INTERGENIC
3R	5785958	3R_5785958_SNP [dm3] 3R_9960236_SNP [dm6]	T	C	1.949e^-6	0.516	INTRON Glut4EF
2L	18858630	2L_18858630_DEL [dm3] 2L_18858630_DEL [dm6]	AATCGGCGACCAT...	A	2.550e^-6	0.516	UPSTREAM CG10602 DOWNSTREAM tup INTRON CG10602 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1
X	15738163	X_15738163_SNP [dm3] X_15844130_SNP [dm6]	C	A	3.088e^-6	0.516	START_GAINED Aats-arg UTR_5_PRIME Aats-arg UPSTREAM CG8578	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Ubx
3R	25091548	3R_25091548_SNP [dm3] 3R_29265826_SNP [dm6]	T	A	3.710e^-6	0.516	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	9716431	3L_9716431_SNP [dm3] 3L_9723331_SNP [dm6]	A	C	3.739e^-6	0.516	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	9716369	3L_9716369_SNP [dm3] 3L_9723269_SNP [dm6]	T	C	4.212e^-6	0.516	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
3L	3547729	3L_3547729_SNP [dm3] 3L_3547729_SNP [dm6]	A	T	4.401e^-6	0.516	INTRON Eip63E
2L	4290845	2L_4290845_SNP [dm3] 2L_4290845_SNP [dm6]	T	C	4.787e^-6	0.516	INTRON tutl
3L	9716322	3L_9716322_SNP [dm3] 3L_9723222_SNP [dm6]	A	T	4.930e^-6	0.516	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
X	15135061	X_15135061_SNP [dm3] X_15241028_SNP [dm6]	G	C	5.245e^-6	0.516	INTERGENIC
3L	7259205	3L_7259205_SNP [dm3] 3L_7266105_SNP [dm6]	C	A	5.398e^-6	0.516	DOWNSTREAM unc-13-4A INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	21909882	2L_21909882_SNP [dm3] 2L_21909882_SNP [dm6]	C	T	5.558e^-6	0.516	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
3L	9715826	3L_9715826_SNP [dm3] 3L_9722726_SNP [dm6]	A	G	5.596e^-6	0.516	SYNONYMOUS_CODING nbs UPSTREAM defl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	9716377	3L_9716377_SNP [dm3] 3L_9723277_SNP [dm6]	T	C	6.002e^-6	0.516	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
3L	3547796	3L_3547796_SNP [dm3] 3L_3547796_SNP [dm6]	T	A	6.480e^-6	0.516	INTRON Eip63E
2L	22020494	2L_22020494_SNP [dm3] 2L_22020494_SNP [dm6]	A	G	7.016e^-6	0.516	DOWNSTREAM CR33987 INTRON tio	TF binding site mE1_TFBS_Trl
3R	5786004	3R_5786004_SNP [dm3] 3R_9960282_SNP [dm6]	C	T	7.118e^-6	0.516	INTRON Glut4EF
3R	5786011	3R_5786011_SNP [dm3] 3R_9960289_SNP [dm6]	T	A	7.468e^-6	0.516	INTRON Glut4EF
3L	9716420	3L_9716420_INS [dm3] 3L_9723320_INS [dm6]	G	TTA	7.545e^-6	0.516	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	5786016	3R_5786016_SNP [dm3] 3R_9960294_SNP [dm6]	C	T	7.686e^-6	0.516	INTRON Glut4EF
3L	7875188	3L_7875188_SNP [dm3] 3L_7882088_SNP [dm6]	A	T	7.987e^-6	0.516	INTRON CG32365
3L	9716375	3L_9716375_SNP [dm3] 3L_9723275_SNP [dm6]	G	T	8.048e^-6	0.516	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2L	16493446	2L_16493446_SNP [dm3] 2L_16493446_SNP [dm6]	C	T	8.377e^-6	0.516	INTRON Tpr2	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3R	5838910	3R_5838910_SNP [dm3] 3R_10013188_SNP [dm6]	A	G	8.499e^-6	0.516	SYNONYMOUS_CODING Mical INTRON Mical
3L	3547681	3L_3547681_SNP [dm3] 3L_3547681_SNP [dm6]	C	G	8.532e^-6	0.516	INTRON Eip63E
2R	16961944	2R_16961944_DEL [dm3] 2R_21074439_DEL [dm6]	TAAATA	T	9.132e^-6	0.522	INTRON Treh
3L	9716422	3L_9716422_SNP [dm3] 3L_9723322_SNP [dm6]	C	T	9.196e^-6	0.522	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	2537242	3L_2537242_SNP [dm3] 3L_2537242_SNP [dm6]	A	G	9.654e^-6	0.532	UPSTREAM Spn INTRON Spn	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	9716433	3L_9716433_SNP [dm3] 3L_9723333_SNP [dm6]	A	T	1.003e^-5	0.537	UPSTREAM defl & 1 other INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	7366142	3R_7366142_SNP [dm3] 3R_11540420_SNP [dm6]	T	G	1.117e^-5	0.553	INTRON dpr4
3R	5759037	3R_5759037_SNP [dm3] 3R_9933315_SNP [dm6]	C	T	1.120e^-5	0.553	INTRON Glut4EF
3R	5769824	3R_5769824_SNP [dm3] 3R_9944102_SNP [dm6]	G	A	1.128e^-5	0.553	UTR_3_PRIME Glut4EF INTRON Glut4EF
3R	5816807	3R_5816807_SNP [dm3] 3R_9991085_SNP [dm6]	A	G	1.151e^-5	0.553	UTR_3_PRIME Glut4EF
3R	5862855	3R_5862855_SNP [dm3] 3R_10037133_SNP [dm6]	G	A	1.216e^-5	0.57	INTRON Mical
3L	3547769	3L_3547769_SNP [dm3] 3L_3547769_SNP [dm6]	T	C	1.336e^-5	0.595	INTRON Eip63E
X	17078271	X_17078271_SNP [dm3] X_17184238_SNP [dm6]	T	C	1.353e^-5	0.595	UPSTREAM CR44026 INTRON baz
3L	1647129	3L_1647129_SNP [dm3] 3L_1647129_SNP [dm6]	A	G	1.405e^-5	0.595	NON_SYNONYMOUS_CODING CG17249 UPSTREAM Bro	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3L	14370112	3L_14370112_SNP [dm3] 3L_14377012_SNP [dm6]	C	A	1.470e^-5	0.595	INTERGENIC
3L	13549795	3L_13549795_SNP [dm3] 3L_13556695_SNP [dm6]	A	G	1.483e^-5	0.595	INTRON bru-3
3R	5877506	3R_5877506_SNP [dm3] 3R_10051784_SNP [dm6]	G	C	1.497e^-5	0.595	SYNONYMOUS_CODING Fancl DOWNSTREAM CG3925	TF binding site mE1_TFBS_cad
2L	8626603	2L_8626603_SNP [dm3] 2L_8626603_SNP [dm6]	G	C	1.522e^-5	0.595	INTRON Sema-1a
3R	5899901	3R_5899901_SNP [dm3] 3R_10074179_SNP [dm6]	A	C	1.535e^-5	0.595	SYNONYMOUS_CODING CG5361 DOWNSTREAM nerfin-2
3L	9716427	3L_9716427_SNP [dm3] 3L_9723327_SNP [dm6]	G	A	1.587e^-5	0.595	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
X	13551185	X_13551185_SNP [dm3] X_13657152_SNP [dm6]	A	C	1.666e^-5	0.595	INTRON NFAT
2R	11575928	2R_11575928_SNP [dm3] 2R_15688423_SNP [dm6]	T	C	1.739e^-5	0.595	SYNONYMOUS_CODING Cep89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	21802210	2L_21802210_SNP [dm3] 2L_21802210_SNP [dm6]	G	A	1.745e^-5	0.595	INTERGENIC
3R	10166354	3R_10166354_SNP [dm3] 3R_14340632_SNP [dm6]	G	A	1.789e^-5	0.595	INTRON NK7.1
3R	5720416	3R_5720416_SNP [dm3] 3R_9894694_SNP [dm6]	T	C	1.828e^-5	0.595	INTRON Glut4EF	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	24152065	3R_24152065_SNP [dm3] 3R_28326343_SNP [dm6]	C	T	1.861e^-5	0.595	UPSTREAM larp INTRON larp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	17693886	2R_17693886_SNP [dm3] 2R_21806381_SNP [dm6]	T	C	1.864e^-5	0.595	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
3L	9716472	3L_9716472_SNP [dm3] 3L_9723372_SNP [dm6]	T	G	1.878e^-5	0.595	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	3967713	3R_3967713_SNP [dm3] 3R_8141991_SNP [dm6]	T	A	1.940e^-5	0.595	UPSTREAM tRNA:R2:84Fa INTERGENIC
3L	3547802	3L_3547802_SNP [dm3] 3L_3547802_SNP [dm6]	C	A	1.943e^-5	0.595	INTRON Eip63E
3L	13549850	3L_13549850_SNP [dm3] 3L_13556750_SNP [dm6]	A	G	1.969e^-5	0.595	INTRON bru-3
2R	6530491	2R_6530491_SNP [dm3] 2R_10642986_SNP [dm6]	C	A	1.993e^-5	0.595	INTRON Git	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	3966171	3R_3966171_SNP [dm3] 3R_8140449_SNP [dm6]	T	G	2.072e^-5	0.595	UPSTREAM tRNA:N5:84F & 2 others DOWNSTREAM tRNA:R2:84Fc & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	892036	X_892036_SNP [dm3] X_998003_SNP [dm6]	T	A	2.120e^-5	0.595	INTERGENIC
2R	11575711	2R_11575711_SNP [dm3] 2R_15688206_SNP [dm6]	G	T	2.131e^-5	0.595	NON_SYNONYMOUS_CODING Cep89 SPLICE_SITE_REGION Cep89 DOWNSTREAM Ranbp11	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	15141159	2L_15141159_SNP [dm3] 2L_15141159_SNP [dm6]	T	C	2.186e^-5	0.595	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	11858178	3R_11858178_SNP [dm3] 3R_16032456_SNP [dm6]	C	T	2.195e^-5	0.595	INTRON pnr	TF binding site mE1_TFBS_inv
2L	6850371	2L_6850371_SNP [dm3] 2L_6850371_SNP [dm6]	T	A	2.207e^-5	0.595	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	17078601	2R_17078601_SNP [dm3] 2R_21191096_SNP [dm6]	A	G	2.214e^-5	0.595	NON_SYNONYMOUS_CODING tud	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	11856703	3R_11856703_SNP [dm3] 3R_16030981_SNP [dm6]	A	G	2.325e^-5	0.595	INTRON pnr
3L	5130681	3L_5130681_SNP [dm3] 3L_5137581_SNP [dm6]	G	A	2.329e^-5	0.595	SYNONYMOUS_CODING CG4611	TF binding site mE1_TFBS_chinmo
3L	9716331	3L_9716331_SNP [dm3] 3L_9723231_SNP [dm6]	C	T	2.340e^-5	0.595	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
3R	3271914	3R_3271914_SNP [dm3] 3R_7446192_SNP [dm6]	G	T	2.354e^-5	0.595	INTERGENIC
2R	10654646	2R_10654646_SNP [dm3] 2R_14767141_SNP [dm6]	G	C	2.355e^-5	0.595	INTRON Spred
3L	7875197	3L_7875197_SNP [dm3] 3L_7882097_SNP [dm6]	T	A	2.363e^-5	0.595	INTRON CG32365
3L	7259208	3L_7259208_SNP [dm3] 3L_7266108_SNP [dm6]	T	C	2.408e^-5	0.595	DOWNSTREAM unc-13-4A INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	15394423	3R_15394423_INS [dm3] 3R_19568701_INS [dm6]	A	AA	2.437e^-5	0.595	UPSTREAM Dys INTRON Dys	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	20906349	3L_20906349_SNP [dm3] 3L_20913249_SNP [dm6]	C	T	2.531e^-5	0.595	DOWNSTREAM CR45733 EXON CR43930
3L	14361935	3L_14361935_SNP [dm3] 3L_14368835_SNP [dm6]	T	C	2.542e^-5	0.595	DOWNSTREAM CG13481 & 1 other INTERGENIC
3R	5786538	3R_5786538_SNP [dm3] 3R_9960816_SNP [dm6]	G	A	2.543e^-5	0.595	INTRON Glut4EF	TF binding site mE1_TFBS_HSA
3R	16988813	3R_16988813_SNP [dm3] 3R_21163091_SNP [dm6]	C	G	2.562e^-5	0.595	UPSTREAM CG5810 INTRON SNF4Agamma
3L	9716464	3L_9716464_SNP [dm3] 3L_9723364_SNP [dm6]	A	T	2.675e^-5	0.595	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	19279601	2R_19279601_SNP [dm3] 2R_23392078_SNP [dm6]	G	A	2.715e^-5	0.595	INTRON CG3530	TF binding site mE1_TFBS_chinmo
X	5615803	X_5615803_DEL [dm3] X_5721770_DEL [dm6]	ATTGTGCA	A	2.738e^-5	0.595	INTRON CG32758
X	5615812	X_5615812_SNP [dm3] X_5721779_SNP [dm6]	C	T	2.738e^-5	0.595	INTRON CG32758
3R	24151899	3R_24151899_SNP [dm3] 3R_28326177_SNP [dm6]	A	T	2.740e^-5	0.595	UTR_5_PRIME larp INTRON larp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	7723496	X_7723496_SNP [dm3] X_7829463_SNP [dm6]	T	C	2.966e^-5	0.595	INTRON CG1402
X	18363771	X_18363771_SNP [dm3] X_18469738_SNP [dm6]	C	T	2.978e^-5	0.595	INTRON CG32547
2R	12545372	2R_12545372_SNP [dm3] 2R_16657867_SNP [dm6]	T	A	2.981e^-5	0.595	INTRON Picot
3L	3547671	3L_3547671_SNP [dm3] 3L_3547671_SNP [dm6]	T	C	3.030e^-5	0.595	INTRON Eip63E
2L	21909898	2L_21909898_DEL [dm3] 2L_21909898_DEL [dm6]	CATAATAGGG	C	3.057e^-5	0.595	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
3R	5882236	3R_5882236_SNP [dm3] 3R_10056514_SNP [dm6]	C	A	3.148e^-5	0.595	UPSTREAM Npc2d INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	5783874	3R_5783874_SNP [dm3] 3R_9958152_SNP [dm6]	C	A	3.178e^-5	0.595	INTRON Glut4EF
2L	12376192	2L_12376192_SNP [dm3] 2L_12376192_SNP [dm6]	A	G	3.188e^-5	0.595	INTRON bru-2
3R	5804593	3R_5804593_SNP [dm3] 3R_9978871_SNP [dm6]	C	G	3.208e^-5	0.595	INTRON Glut4EF	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	9716328	3L_9716328_SNP [dm3] 3L_9723228_SNP [dm6]	C	T	3.230e^-5	0.595	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2R	19410022	2R_19410022_SNP [dm3] 2R_23522499_SNP [dm6]	A	G	3.232e^-5	0.595	INTRON RabX1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
X	8094483	X_8094483_SNP [dm3] X_8200450_SNP [dm6]	A	C	3.241e^-5	0.595	INTRON sdt
3R	13937696	3R_13937696_SNP [dm3] 3R_18111974_SNP [dm6]	A	G	3.311e^-5	0.595	INTRON sr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	16763110	3R_16763110_SNP [dm3] 3R_20937388_SNP [dm6]	A	G	3.314e^-5	0.595	INTRON CG31191
2L	20710097	2L_20710097_SNP [dm3] 2L_20710097_SNP [dm6]	G	T	3.460e^-5	0.595	INTRON Hr38 EXON CR44187

Showing 1 to 100 of 1,000 entries

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GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=4.868e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_2L_t	0.06031

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	7.7122	0.0212
In_3R_Mo	5.6166	0.0603

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2029 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	3268396	3R_3268396_SNP [dm3] 3R_7442674_SNP [dm6]	T	A	2.883e^-6	0.889	DOWNSTREAM CG14598 INTERGENIC
3L	2894083	3L_2894083_DEL [dm3] 3L_2894083_DEL [dm6]	TT	G	3.029e^-6	0.889	UPSTREAM Shab INTERGENIC
2R	16961944	2R_16961944_DEL [dm3] 2R_21074439_DEL [dm6]	TAAATA	T	5.731e^-6	0.889	INTRON Treh
2L	15307291	2L_15307291_SNP [dm3] 2L_15307291_SNP [dm6]	G	T	6.375e^-6	0.889	INTERGENIC
3L	9715826	3L_9715826_SNP [dm3] 3L_9722726_SNP [dm6]	A	G	6.904e^-6	0.889	SYNONYMOUS_CODING nbs UPSTREAM defl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	901595	2R_901595_INS [dm3] 2R_5014090_INS [dm6]	T	TAT	7.607e^-6	0.889	INTRON Ir41a
2R	17725771	2R_17725771_SNP [dm3] 2R_21838266_SNP [dm6]	C	T	7.735e^-6	0.889	NON_SYNONYMOUS_CODING CG4372
2R	16923351	2R_16923351_DEL [dm3] 2R_21035846_DEL [dm6]	TT	T	8.261e^-6	0.889	INTERGENIC
2R	19564911	2R_19564911_SNP [dm3] 2R_23677388_SNP [dm6]	T	A	8.967e^-6	0.889	INTRON Pde8	TF binding site mE1_TFBS_cad
2L	7842500	2L_7842500_SNP [dm3] 2L_7842500_SNP [dm6]	G	A	9.411e^-6	0.889	INTERGENIC
3R	16988813	3R_16988813_SNP [dm3] 3R_21163091_SNP [dm6]	C	G	9.422e^-6	0.889	UPSTREAM CG5810 INTRON SNF4Agamma
3L	4652284	3L_4652284_SNP [dm3] 3L_4652284_SNP [dm6]	T	G	9.448e^-6	0.889	INTRON axo
3L	9715763	3L_9715763_SNP [dm3] 3L_9722663_SNP [dm6]	C	T	9.479e^-6	0.889	NON_SYNONYMOUS_CODING nbs UPSTREAM defl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	15307422	2L_15307422_SNP [dm3] 2L_15307422_SNP [dm6]	G	C	1.002e^-5	0.889	INTERGENIC
2R	5509260	2R_5509260_SNP [dm3] 2R_9621755_SNP [dm6]	G	C	1.139e^-5	0.889	UPSTREAM mir-307a DOWNSTREAM mir-307b INTRON Mmp2
2L	9570400	2L_9570400_SNP [dm3] 2L_9570400_SNP [dm6]	A	G	1.385e^-5	0.889	UTR_5_PRIME CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	21896719	3R_21896719_SNP [dm3] 3R_26070997_SNP [dm6]	C	T	1.418e^-5	0.889	EXON CR44950
X	18389071	X_18389071_SNP [dm3] X_18495038_SNP [dm6]	T	C	1.469e^-5	0.889	UPSTREAM CG15043 DOWNSTREAM GalNAc-T2 & 1 other INTERGENIC
2L	8807137	2L_8807137_SNP [dm3] 2L_8807137_SNP [dm6]	T	C	1.525e^-5	0.889	INTERGENIC
3L	11318516	3L_11318516_SNP [dm3] 3L_11325416_SNP [dm6]	T	C	1.531e^-5	0.889	UPSTREAM CR44723 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
X	16539871	X_16539871_INS [dm3] X_16645838_INS [dm6]	T	TT	1.558e^-5	0.889	INTRON mthl1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2L	18328268	2L_18328268_SNP [dm3] 2L_18328268_SNP [dm6]	A	T	1.685e^-5	0.889	INTRON Fas3
X	19871242	X_19871242_SNP [dm3] X_19977209_SNP [dm6]	A	G	1.698e^-5	0.889	INTERGENIC
X	17078271	X_17078271_SNP [dm3] X_17184238_SNP [dm6]	T	C	1.760e^-5	0.889	UPSTREAM CR44026 INTRON baz
2L	13610291	2L_13610291_SNP [dm3] 2L_13610291_SNP [dm6]	C	T	1.848e^-5	0.889	NON_SYNONYMOUS_CODING kuz DOWNSTREAM mir-2489
2L	5395011	2L_5395011_SNP [dm3] 2L_5395011_SNP [dm6]	C	T	1.852e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
3L	9716369	3L_9716369_SNP [dm3] 3L_9723269_SNP [dm6]	T	C	1.890e^-5	0.889	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
3L	14370112	3L_14370112_SNP [dm3] 3L_14377012_SNP [dm6]	C	A	1.915e^-5	0.889	INTERGENIC
2R	16856340	2R_16856340_SNP [dm3] 2R_20968835_SNP [dm6]	A	C	2.004e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	9570147	2L_9570147_INS [dm3] 2L_9570147_INS [dm6]	A	AC	2.059e^-5	0.889	UPSTREAM CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16133838	X_16133838_SNP [dm3] X_16239805_SNP [dm6]	T	A	2.109e^-5	0.889	INTERGENIC
2L	18328109	2L_18328109_SNP [dm3] 2L_18328109_SNP [dm6]	C	G	2.148e^-5	0.889	INTRON Fas3
2L	9570296	2L_9570296_SNP [dm3] 2L_9570296_SNP [dm6]	A	C	2.172e^-5	0.889	UTR_5_PRIME CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	22020382	2L_22020382_SNP [dm3] 2L_22020382_SNP [dm6]	G	T	2.198e^-5	0.889	DOWNSTREAM CR33987 INTRON tio	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	9570169	2L_9570169_SNP [dm3] 2L_9570169_SNP [dm6]	A	G	2.333e^-5	0.889	UPSTREAM CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	9202302	3L_9202302_SNP [dm3] 3L_9209202_SNP [dm6]	T	G	2.490e^-5	0.889	UPSTREAM Slc45-1 INTERGENIC
3R	1592708	3R_1592708_SNP [dm3] 3R_5766986_SNP [dm6]	A	T	2.533e^-5	0.889	INTRON CG2082	TF binding site mE1_TFBS_cad
2R	11575928	2R_11575928_SNP [dm3] 2R_15688423_SNP [dm6]	T	C	2.544e^-5	0.889	SYNONYMOUS_CODING Cep89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	5346953	2L_5346953_SNP [dm3] 2L_5346953_SNP [dm6]	T	A	2.573e^-5	0.889	SYNONYMOUS_CODING nompC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	18885261	2L_18885261_SNP [dm3] 2L_18885261_SNP [dm6]	C	G	2.588e^-5	0.889	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	12571601	2L_12571601_SNP [dm3] 2L_12571601_SNP [dm6]	G	A	2.592e^-5	0.889	UPSTREAM CR44598 EXON CR44597
2L	21802210	2L_21802210_SNP [dm3] 2L_21802210_SNP [dm6]	G	A	2.697e^-5	0.889	INTERGENIC
2R	16923357	2R_16923357_SNP [dm3] 2R_21035852_SNP [dm6]	C	T	2.710e^-5	0.889	INTERGENIC
2L	8626603	2L_8626603_SNP [dm3] 2L_8626603_SNP [dm6]	G	C	2.723e^-5	0.889	INTRON Sema-1a
3L	1317457	3L_1317457_SNP [dm3] 3L_1317457_SNP [dm6]	G	A	2.935e^-5	0.889	SYNONYMOUS_CODING CG9153	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	8587669	3R_8587669_SNP [dm3] 3R_12761947_SNP [dm6]	G	C	2.937e^-5	0.889	INTRON beat-Vc
3R	19776867	3R_19776867_SNP [dm3] 3R_23951145_SNP [dm6]	G	A	2.944e^-5	0.889	DOWNSTREAM Aats-glupro INTERGENIC
2L	21851919	2L_21851919_INS [dm3] 2L_21851919_INS [dm6]	T	TTCT	2.966e^-5	0.889	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3R	3271914	3R_3271914_SNP [dm3] 3R_7446192_SNP [dm6]	G	T	3.017e^-5	0.889	INTERGENIC
2L	9570077	2L_9570077_DEL [dm3] 2L_9570077_DEL [dm6]	ATTAATAGTTGA...	A	3.066e^-5	0.889	UPSTREAM CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	19861257	2R_19861257_SNP [dm3] 2R_23973734_SNP [dm6]	A	G	3.077e^-5	0.889	INTRON mr	TF binding site mE1_TFBS_sens
2L	18328372	2L_18328372_SNP [dm3] 2L_18328372_SNP [dm6]	C	G	3.118e^-5	0.889	INTRON Fas3
3R	16989117	3R_16989117_SNP [dm3] 3R_21163395_SNP [dm6]	A	T	3.193e^-5	0.889	UPSTREAM CG5810 INTRON SNF4Agamma
X	20218412	X_20218412_SNP [dm3] X_20347385_SNP [dm6]	T	A	3.204e^-5	0.889	INTERGENIC
2L	9562535	2L_9562535_SNP [dm3] 2L_9562535_SNP [dm6]	T	C	3.259e^-5	0.889	INTRON jp
3L	7138315	3L_7138315_SNP [dm3] 3L_7145215_SNP [dm6]	G	A	3.362e^-5	0.889	INTRON corn
X	19869871	X_19869871_SNP [dm3] X_19975838_SNP [dm6]	C	T	3.378e^-5	0.889	INTERGENIC
2L	9564119	2L_9564119_SNP [dm3] 2L_9564119_SNP [dm6]	A	G	3.389e^-5	0.889	INTRON jp
2L	9570118	2L_9570118_SNP [dm3] 2L_9570118_SNP [dm6]	A	T	3.402e^-5	0.889	UPSTREAM CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	20218269	X_20218269_SNP [dm3] X_20347242_SNP [dm6]	C	A	3.452e^-5	0.889	INTERGENIC
3L	20906349	3L_20906349_SNP [dm3] 3L_20913249_SNP [dm6]	C	T	3.455e^-5	0.889	DOWNSTREAM CR45733 EXON CR43930
3R	1587773	3R_1587773_SNP [dm3] 3R_5762051_SNP [dm6]	A	T	3.700e^-5	0.889	INTRON CG2082
3L	9716377	3L_9716377_SNP [dm3] 3L_9723277_SNP [dm6]	T	C	3.722e^-5	0.889	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Ubx
2L	9569454	2L_9569454_SNP [dm3] 2L_9569454_SNP [dm6]	G	C	3.728e^-5	0.889	UPSTREAM CR44149 & 1 other INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3L	3027213	3L_3027213_SNP [dm3] 3L_3027213_SNP [dm6]	C	T	3.841e^-5	0.889	UPSTREAM aly INTERGENIC
3L	332002	3L_332002_SNP [dm3] 3L_332002_SNP [dm6]	T	A	3.944e^-5	0.889	UTR_5_PRIME mthl9 DOWNSTREAM mthl10 INTRON Ptpmeg	TF binding site mE1_TFBS_Trl
2L	16493517	2L_16493517_SNP [dm3] 2L_16493517_SNP [dm6]	T	G	4.015e^-5	0.889	INTRON Tpr2	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	7485366	3L_7485366_SNP [dm3] 3L_7492266_SNP [dm6]	A	T	4.032e^-5	0.889	NON_SYNONYMOUS_CODING Cyp316a1
3L	7259205	3L_7259205_SNP [dm3] 3L_7266105_SNP [dm6]	C	A	4.044e^-5	0.889	DOWNSTREAM unc-13-4A INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	19859985	2R_19859985_SNP [dm3] 2R_23972462_SNP [dm6]	A	T	4.046e^-5	0.889	UTR_5_PRIME mr DOWNSTREAM CG3065	TF binding site mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_ttk mE1_TFBS_Ubx
2L	9570049	2L_9570049_SNP [dm3] 2L_9570049_SNP [dm6]	C	G	4.103e^-5	0.889	UPSTREAM CG3838 INTRON CG3838	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8911214	2L_8911214_SNP [dm3] 2L_8911214_SNP [dm6]	T	C	4.137e^-5	0.889	INTRON CG34398
3L	337491	3L_337491_SNP [dm3] 3L_337491_SNP [dm6]	C	T	4.205e^-5	0.889	INTRON Ptpmeg & 1 other
2R	19873759	2R_19873759_SNP [dm3] 2R_23986236_SNP [dm6]	T	G	4.254e^-5	0.889	UPSTREAM CG30178 INTRON Phm
2L	2275044	2L_2275044_SNP [dm3] 2L_2275044_SNP [dm6]	T	A	4.273e^-5	0.889	DOWNSTREAM CR43753 INTRON CR43753
2R	16923365	2R_16923365_SNP [dm3] 2R_21035860_SNP [dm6]	C	G	4.285e^-5	0.889	INTERGENIC
3R	10507897	3R_10507897_SNP [dm3] 3R_14682175_SNP [dm6]	G	C	4.351e^-5	0.889	INTRON Meltrin	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
X	18222879	X_18222879_SNP [dm3] X_18328846_SNP [dm6]	A	C	4.353e^-5	0.889	INTRON CG6123
3L	12068858	3L_12068858_SNP [dm3] 3L_12075758_SNP [dm6]	A	G	4.375e^-5	0.889	INTRON Sema-5c
3L	7138322	3L_7138322_SNP [dm3] 3L_7145222_SNP [dm6]	A	G	4.377e^-5	0.889	INTRON corn
2R	10578635	2R_10578635_SNP [dm3] 2R_14691130_SNP [dm6]	T	C	4.692e^-5	0.889	INTRON mspo
X	13314029	X_13314029_SNP [dm3] X_13419996_SNP [dm6]	A	G	4.706e^-5	0.889	SYNONYMOUS_CODING Set2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	1243265	3L_1243265_SNP [dm3] 3L_1243265_SNP [dm6]	C	T	4.719e^-5	0.889	SYNONYMOUS_CODING Klp61F
3L	9716431	3L_9716431_SNP [dm3] 3L_9723331_SNP [dm6]	A	C	4.757e^-5	0.889	UPSTREAM defl & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	16361229	2R_16361229_SNP [dm3] 2R_20473724_SNP [dm6]	G	T	4.759e^-5	0.889	INTRON CG12484
X	17076829	X_17076829_DEL [dm3] X_17182796_DEL [dm6]	TACGGTT	T	4.790e^-5	0.889	DOWNSTREAM CR44026 INTRON baz
2L	21866518	2L_21866518_SNP [dm3] 2L_21866518_SNP [dm6]	A	G	4.865e^-5	0.889	UPSTREAM CR44917 & 1 other DOWNSTREAM CR44919 INTRON CR44917	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13554710	3L_13554710_SNP [dm3] 3L_13561610_SNP [dm6]	A	G	4.993e^-5	0.889	INTRON bru-3	TF binding site mE1_TFBS_chinmo
2L	10586732	2L_10586732_SNP [dm3] 2L_10586732_SNP [dm6]	G	A	5.042e^-5	0.889	INTRON Trim9	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	13314040	X_13314040_SNP [dm3] X_13420007_SNP [dm6]	T	C	5.059e^-5	0.889	NON_SYNONYMOUS_CODING Set2	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	16727046	3L_16727046_SNP [dm3] 3L_16733946_SNP [dm6]	T	A	5.092e^-5	0.889	INTRON CG9701
3R	14335072	3R_14335072_INS [dm3] 3R_18509350_INS [dm6]	T	TTT	5.117e^-5	0.889	INTRON fru
2R	19873807	2R_19873807_SNP [dm3] 2R_23986284_SNP [dm6]	G	A	5.165e^-5	0.889	SYNONYMOUS_CODING Phm UPSTREAM CG30178	TF binding site mE1_TFBS_HSA
3R	1670042	3R_1670042_DEL [dm3] 3R_5844320_DEL [dm6]	TCC	G	5.230e^-5	0.889	INTRON CG1213
2R	12384618	2R_12384618_SNP [dm3] 2R_16497113_SNP [dm6]	C	G	5.270e^-5	0.889	NON_SYNONYMOUS_CODING CG7813
X	9498848	X_9498848_SNP [dm3] X_9604815_SNP [dm6]	G	A	5.290e^-5	0.889	UTR_3_PRIME Lst8 DOWNSTREAM Gga
X	9498923	X_9498923_SNP [dm3] X_9604890_SNP [dm6]	G	A	5.290e^-5	0.889	SYNONYMOUS_CODING Lst8 DOWNSTREAM Gga
X	5743499	X_5743499_SNP [dm3] X_5849466_SNP [dm6]	A	C	5.396e^-5	0.889	INTERGENIC
2L	9563571	2L_9563571_SNP [dm3] 2L_9563571_SNP [dm6]	A	G	5.406e^-5	0.889	INTRON jp
2R	15715160	2R_15715160_SNP [dm3] 2R_19827655_SNP [dm6]	G	A	5.412e^-5	0.889	NON_SYNONYMOUS_CODING Toll-7	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens

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Phenotype distribution and association to known covariates

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GWAS results