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=5.741e^-5)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT 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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2429 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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	26176018	3R_26176018_SNP [dm3] 3R_30350296_SNP [dm6]	C	A	3.859e^-7	0.659	INTRON hdc
3R	14094242	3R_14094242_SNP [dm3] 3R_18268520_SNP [dm6]	T	C	1.586e^-6	0.659	INTRON CG18599
3L	2545668	3L_2545668_DEL [dm3] 3L_2545668_DEL [dm6]	TAAATTAAAGGCTTTGT...	T	1.696e^-6	0.659	INTRON Spn
2L	14795131	2L_14795131_DEL [dm3] 2L_14795131_DEL [dm6]	CC	C	1.985e^-6	0.659	UTR_3_PRIME CG18420
3R	14094271	3R_14094271_SNP [dm3] 3R_18268549_SNP [dm6]	A	G	2.810e^-6	0.659	INTRON CG18599
3R	26088906	3R_26088906_SNP [dm3] 3R_30263184_SNP [dm6]	C	T	3.594e^-6	0.659	INTERGENIC
2R	3346733	2R_3346733_DEL [dm3] 2R_7459228_DEL [dm6]	TA	T	4.222e^-6	0.659	UPSTREAM Inos DOWNSTREAM CG11141 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	10530153	2L_10530153_SNP [dm3] 2L_10530153_SNP [dm6]	T	C	4.583e^-6	0.659	SYNONYMOUS_CODING Lip4
2L	7900509	2L_7900509_SNP [dm3] 2L_7900509_SNP [dm6]	A	C	5.418e^-6	0.659	INTRON Snoo
2L	3378046	2L_3378046_SNP [dm3] 2L_3378046_SNP [dm6]	A	T	5.781e^-6	0.659	SYNONYMOUS_CODING Ptpa	TF binding site mE1_TFBS_sens
X	12584129	X_12584129_SNP [dm3] X_12690096_SNP [dm6]	C	A	6.527e^-6	0.659	SYNONYMOUS_CODING Smr	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_kni BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	9258817	3L_9258817_SNP [dm3] 3L_9265717_SNP [dm6]	A	C	6.784e^-6	0.659	INTRON GluRIB
2L	17775496	2L_17775496_SNP [dm3] 2L_17775496_SNP [dm6]	T	A	7.233e^-6	0.659	INTRON CadN
3R	18636393	3R_18636393_SNP [dm3] 3R_22810671_SNP [dm6]	T	C	8.263e^-6	0.659	INTERGENIC
3R	13242326	3R_13242326_SNP [dm3] 3R_17416604_SNP [dm6]	T	A	9.278e^-6	0.659	UPSTREAM CG33333 DOWNSTREAM CG5866 INTERGENIC
3R	26667352	3R_26667352_SNP [dm3] 3R_30841630_SNP [dm6]	T	A	9.309e^-6	0.659	UTR_3_PRIME CG15544
2L	7994399	2L_7994399_SNP [dm3] 2L_7994399_SNP [dm6]	T	C	9.431e^-6	0.659	UTR_3_PRIME CG7227 UPSTREAM pes & 1 other DOWNSTREAM CG7227	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_en mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_jumu mE1_TFBS_Trl
3R	25476842	3R_25476842_SNP [dm3] 3R_29651120_SNP [dm6]	C	T	9.573e^-6	0.659	INTRON Dop1R2	TF binding site mE1_TFBS_chinmo
X	10568445	X_10568445_SNP [dm3] X_10674412_SNP [dm6]	A	C	9.660e^-6	0.659	UPSTREAM CG12637 INTRON X11Lbeta	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12861426	2R_12861426_SNP [dm3] 2R_16973921_SNP [dm6]	T	C	9.861e^-6	0.659	UPSTREAM Cbp53E INTERGENIC
2L	448813	2L_448813_SNP [dm3] 2L_448813_SNP [dm6]	T	G	1.072e^-5	0.659	UTR_3_PRIME crq DOWNSTREAM ex
3L	18352450	3L_18352450_SNP [dm3] 3L_18359350_SNP [dm6]	T	A	1.083e^-5	0.659	INTERGENIC
X	5872642	X_5872642_SNP [dm3] X_5978609_SNP [dm6]	G	A	1.089e^-5	0.659	INTRON Grip
2R	12074021	2R_12074021_SNP [dm3] 2R_16186516_SNP [dm6]	C	A	1.130e^-5	0.659	UPSTREAM clu & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_Ubx
2R	9637295	2R_9637295_SNP [dm3] 2R_13749790_SNP [dm6]	G	A	1.154e^-5	0.659	DOWNSTREAM fas INTERGENIC
3L	1081436	3L_1081436_SNP [dm3] 3L_1081436_SNP [dm6]	A	G	1.198e^-5	0.659	INTRON bab1
3R	19649746	3R_19649746_SNP [dm3] 3R_23824024_SNP [dm6]	T	C	1.322e^-5	0.659	INTRON CG34355
2L	7986113	2L_7986113_SNP [dm3] 2L_7986113_SNP [dm6]	T	C	1.419e^-5	0.659	DOWNSTREAM pes INTRON CG7231	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	12073056	2R_12073056_SNP [dm3] 2R_16185551_SNP [dm6]	A	G	1.508e^-5	0.659	SYNONYMOUS_CODING CG8441 DOWNSTREAM Lis-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
X	5736658	X_5736658_SNP [dm3] X_5842625_SNP [dm6]	C	T	1.530e^-5	0.659	INTERGENIC
3L	14269828	3L_14269828_SNP [dm3] 3L_14276728_SNP [dm6]	T	C	1.532e^-5	0.659	INTRON fz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2L	7818857	2L_7818857_SNP [dm3] 2L_7818857_SNP [dm6]	C	G	1.533e^-5	0.659	SYNONYMOUS_CODING LanB1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	4897079	2L_4897079_SNP [dm3] 2L_4897079_SNP [dm6]	A	G	1.533e^-5	0.659	INTRON CG3036
3R	26871778	3R_26871778_SNP [dm3] 3R_31046056_SNP [dm6]	G	A	1.550e^-5	0.659	UPSTREAM CG33920 INTRON CanA1	TF binding site BDTNP1_TFBS_prd
3L	12374733	3L_12374733_SNP [dm3] 3L_12381633_SNP [dm6]	T	G	1.576e^-5	0.659	INTRON Ncc69	TF binding site mE1_TFBS_inv
2L	17778779	2L_17778779_DEL [dm3] 2L_17778779_DEL [dm6]	CGG	C	1.586e^-5	0.659	UPSTREAM CadN INTERGENIC	TF binding site mE1_TFBS_Trl
3L	767649	3L_767649_SNP [dm3] 3L_767649_SNP [dm6]	T	C	1.597e^-5	0.659	INTERGENIC
X	18464207	X_18464207_SNP [dm3] X_18570174_SNP [dm6]	A	C	1.654e^-5	0.659	INTRON Bx	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo
2L	7900233	2L_7900233_SNP [dm3] 2L_7900233_SNP [dm6]	C	T	1.656e^-5	0.659	INTRON Snoo
X	10625028	X_10625028_INS [dm3] X_10730995_INS [dm6]	T	TC	1.673e^-5	0.659	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2L	12502809	2L_12502809_SNP [dm3] 2L_12502809_SNP [dm6]	T	G	1.752e^-5	0.659	INTRON bun
3L	4726377	3L_4726377_SNP [dm3] 3L_4726377_SNP [dm6]	T	C	1.766e^-5	0.659	INTRON RhoGEF64C
2L	9286685	2L_9286685_SNP [dm3] 2L_9286685_SNP [dm6]	T	C	1.822e^-5	0.659	INTRON Ggamma30A
2L	7900200	2L_7900200_SNP [dm3] 2L_7900200_SNP [dm6]	T	C	1.827e^-5	0.659	INTRON Snoo
2L	4132014	2L_4132014_SNP [dm3] 2L_4132014_SNP [dm6]	C	T	2.022e^-5	0.659	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	19573478	2R_19573478_SNP [dm3] 2R_23685955_SNP [dm6]	C	T	2.032e^-5	0.659	UPSTREAM l_2_efl INTRON St3
2R	16443782	2R_16443782_SNP [dm3] 2R_20556277_SNP [dm6]	C	T	2.060e^-5	0.659	UPSTREAM lms INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	11649398	3L_11649398_SNP [dm3] 3L_11656298_SNP [dm6]	T	C	2.080e^-5	0.659	UPSTREAM mir-274 INTRON CG32085
2R	14994295	2R_14994295_SNP [dm3] 2R_19106790_SNP [dm6]	G	A	2.125e^-5	0.659	INTRON 5-HT1A
2R	12073113	2R_12073113_SNP [dm3] 2R_16185608_SNP [dm6]	C	T	2.170e^-5	0.659	SYNONYMOUS_CODING CG8441 UPSTREAM clu DOWNSTREAM Lis-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3L	9258803	3L_9258803_SNP [dm3] 3L_9265703_SNP [dm6]	G	T	2.255e^-5	0.659	INTRON GluRIB
2L	9888653	2L_9888653_SNP [dm3] 2L_9888653_SNP [dm6]	A	C	2.273e^-5	0.659	INTRON FKBP59	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	12588392	2L_12588392_SNP [dm3] 2L_12588392_SNP [dm6]	A	G	2.289e^-5	0.659	INTRON nub
3R	13210214	3R_13210214_SNP [dm3] 3R_17384492_SNP [dm6]	A	T	2.309e^-5	0.659	INTRON Brf & 1 other
3L	12981081	3L_12981081_SNP [dm3] 3L_12987981_SNP [dm6]	T	A	2.313e^-5	0.659	INTERGENIC
2R	12073825	2R_12073825_DEL [dm3] 2R_16186320_DEL [dm6]	CCTCAACGACGC...	A	2.331e^-5	0.659	UPSTREAM clu & 1 other INTRON CG8441	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2L	7900235	2L_7900235_SNP [dm3] 2L_7900235_SNP [dm6]	C	G	2.334e^-5	0.659	INTRON Snoo
2L	12616488	2L_12616488_SNP [dm3] 2L_12616488_SNP [dm6]	T	C	2.342e^-5	0.659	INTRON Ref2 & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3R	18129037	3R_18129037_SNP [dm3] 3R_22303315_SNP [dm6]	A	G	2.343e^-5	0.659	INTRON CG7084
3L	9258799	3L_9258799_SNP [dm3] 3L_9265699_SNP [dm6]	A	C	2.398e^-5	0.659	INTRON GluRIB
3R	13210218	3R_13210218_DEL [dm3] 3R_17384496_DEL [dm6]	TACGCATCAA	T	2.448e^-5	0.659	INTRON Brf & 1 other
3R	13210266	3R_13210266_SNP [dm3] 3R_17384544_SNP [dm6]	A	T	2.448e^-5	0.659	INTRON Brf & 1 other
X	6484376	X_6484376_SNP [dm3] X_6590343_SNP [dm6]	A	G	2.474e^-5	0.659	SYNONYMOUS_CODING CG17717 UPSTREAM Pat1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	7986378	2L_7986378_SNP [dm3] 2L_7986378_SNP [dm6]	C	A	2.483e^-5	0.659	SYNONYMOUS_CODING CG7231 DOWNSTREAM pes
3R	19649763	3R_19649763_INS [dm3] 3R_23824041_INS [dm6]	T	TGT	2.483e^-5	0.659	INTRON CG34355
3R	25261801	3R_25261801_SNP [dm3] 3R_29436079_SNP [dm6]	T	A	2.505e^-5	0.659	INTRON Ptp99A
3R	26176121	3R_26176121_SNP [dm3] 3R_30350399_SNP [dm6]	G	C	2.526e^-5	0.659	INTRON hdc
2L	3377824	2L_3377824_SNP [dm3] 2L_3377824_SNP [dm6]	T	C	2.578e^-5	0.659	INTRON Ptpa	TF binding site mE1_TFBS_sens
3R	13210235	3R_13210235_DEL [dm3] 3R_17384513_DEL [dm6]	TCCCTGTAAAA...	T	2.592e^-5	0.659	INTRON Brf & 1 other
3R	13210256	3R_13210256_MNP [dm3] 3R_17384534_MNP [dm6]	CGAC	TTTA	2.592e^-5	0.659	INTRON Brf & 1 other
2R	11817318	2R_11817318_DEL [dm3] 2R_15929813_DEL [dm6]	GA	G	2.612e^-5	0.659	INTRON bdg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	13226496	3R_13226496_SNP [dm3] 3R_17400774_SNP [dm6]	A	G	2.651e^-5	0.659	INTRON Sur-8	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA
3R	18474269	3R_18474269_SNP [dm3] 3R_22648547_SNP [dm6]	G	T	2.653e^-5	0.659	INTRON CG45058
3R	19649740	3R_19649740_SNP [dm3] 3R_23824018_SNP [dm6]	T	G	2.655e^-5	0.659	INTRON CG34355
2L	12587759	2L_12587759_SNP [dm3] 2L_12587759_SNP [dm6]	A	T	2.683e^-5	0.659	UTR_5_PRIME nub	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	4132068	2L_4132068_SNP [dm3] 2L_4132068_SNP [dm6]	T	G	2.718e^-5	0.659	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	10531508	3R_10531508_SNP [dm3] 3R_14705786_SNP [dm6]	G	A	2.742e^-5	0.659	INTRON kibra
2L	7986468	2L_7986468_SNP [dm3] 2L_7986468_SNP [dm6]	C	T	2.755e^-5	0.659	SYNONYMOUS_CODING CG7231 DOWNSTREAM pes
3R	180809	3R_180809_SNP [dm3] 3R_4355087_SNP [dm6]	T	A	2.776e^-5	0.659	INTERGENIC
2R	12073840	2R_12073840_SNP [dm3] 2R_16186335_SNP [dm6]	T	A	2.836e^-5	0.66	UPSTREAM clu & 1 other INTRON CG8441	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2R	9591743	2R_9591743_SNP [dm3] 2R_13704238_SNP [dm6]	T	C	2.853e^-5	0.66	INTRON fas
2L	13236971	2L_13236971_SNP [dm3] 2L_13236971_SNP [dm6]	G	A	2.884e^-5	0.66	INTRON CG5867
3R	25261852	3R_25261852_INS [dm3] 3R_29436130_INS [dm6]	T	TAAACTT	3.038e^-5	0.674	INTRON Ptp99A
3R	14094198	3R_14094198_SNP [dm3] 3R_18268476_SNP [dm6]	G	A	3.051e^-5	0.674	INTRON CG18599
2L	17778773	2L_17778773_DEL [dm3] 2L_17778773_DEL [dm6]	TAAAA	T	3.059e^-5	0.674	UPSTREAM CadN INTERGENIC	TF binding site mE1_TFBS_Trl
2R	19346678	2R_19346678_INS [dm3] 2R_23459155_INS [dm6]	T	TT	3.102e^-5	0.674	UPSTREAM skpF INTRON CG43795
3R	26176100	3R_26176100_SNP [dm3] 3R_30350378_SNP [dm6]	C	A	3.159e^-5	0.674	INTRON hdc
X	10568569	X_10568569_SNP [dm3] X_10674536_SNP [dm6]	G	C	3.195e^-5	0.674	INTRON X11Lbeta	TF binding site BDTNP1_TFBS_twi
3L	7063391	3L_7063391_SNP [dm3] 3L_7070291_SNP [dm6]	G	A	3.198e^-5	0.674	INTRON CG8641
2R	11372415	2R_11372415_INS [dm3] 2R_15484910_INS [dm6]	G	GTCTTCG	3.235e^-5	0.674	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_Trl
2L	8994078	2L_8994078_SNP [dm3] 2L_8994078_SNP [dm6]	G	A	3.356e^-5	0.685	UTR_3_PRIME alien UPSTREAM CG17906 DOWNSTREAM CG9555 & 1 other
3L	10369405	3L_10369405_SNP [dm3] 3L_10376305_SNP [dm6]	T	A	3.398e^-5	0.685	INTERGENIC
3L	12494005	3L_12494005_SNP [dm3] 3L_12500905_SNP [dm6]	C	T	3.456e^-5	0.685	SYNONYMOUS_CODING CG10638 UPSTREAM CG10681 DOWNSTREAM CR43868 INTRON CG10638
3L	12374674	3L_12374674_DEL [dm3] 3L_12381574_DEL [dm6]	GAAATTCTTTAACAAGGCGA...	G	3.468e^-5	0.685	INTRON Ncc69	TF binding site mE1_TFBS_inv
X	6119168	X_6119168_SNP [dm3] X_6225135_SNP [dm6]	C	G	3.583e^-5	0.685	UTR_5_PRIME sqh UPSTREAM sqh & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2R	12021871	2R_12021871_SNP [dm3] 2R_16134366_SNP [dm6]	G	A	3.603e^-5	0.685	INTRON spin	TF binding site mE1_TFBS_inv
2L	12702451	2L_12702451_SNP [dm3] 2L_12702451_SNP [dm6]	C	A	3.666e^-5	0.685	SYNONYMOUS_CODING CG5776	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	19931882	2R_19931882_SNP [dm3] 2R_24044359_SNP [dm6]	A	T	3.688e^-5	0.685	UTR_3_PRIME IntS1 DOWNSTREAM tsr	TF binding site BDTNP1_TFBS_dl
3L	12335182	3L_12335182_SNP [dm3] 3L_12342082_SNP [dm6]	A	C	3.733e^-5	0.685	INTRON CrzR
2R	12073844	2R_12073844_SNP [dm3] 2R_16186339_SNP [dm6]	A	T	3.758e^-5	0.685	UPSTREAM clu & 1 other INTRON CG8441	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

lsm_Week3_Fecundity phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results