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=8.341e^-12)
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

7930 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
2R	13588913	2R_13588913_SNP [dm3] 2R_17701408_SNP [dm6]	A	T	2.746e^-11	4.458e^-5	UPSTREAM snoRNA:Me28S-G3277a & 3 others DOWNSTREAM snoRNA:U29:54Ec & 3 others EXON Uhg1
2R	12478738	2R_12478738_SNP [dm3] 2R_16591233_SNP [dm6]	C	T	4.833e^-11	4.458e^-5	SYNONYMOUS_CODING CG8306	TF binding site mE1_TFBS_sens
2R	8904062	2R_8904062_SNP [dm3] 2R_13016557_SNP [dm6]	A	C	2.330e^-10	1.433e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	11636218	2R_11636218_SNP [dm3] 2R_15748713_SNP [dm6]	C	G	3.621e^-10	1.670e^-4	INTRON CG30089	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	6555950	2R_6555950_SNP [dm3] 2R_10668445_SNP [dm6]	A	G	5.007e^-10	1.848e^-4	INTERGENIC
3R	9630054	3R_9630054_SNP [dm3] 3R_13804332_SNP [dm6]	G	T	6.796e^-10	2.090e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9517247	2L_9517247_SNP [dm3] 2L_9517247_SNP [dm6]	T	G	8.151e^-10	2.148e^-4	SYNONYMOUS_CODING CG33298
3R	26076930	3R_26076930_SNP [dm3] 3R_30251208_SNP [dm6]	G	T	9.748e^-10	2.248e^-4	DOWNSTREAM CG34299 INTRON CG9682
2L	12708664	2L_12708664_DEL [dm3] 2L_12708664_DEL [dm6]	ATTGTTAAAGACATATTAAC...	A	1.599e^-9	3.253e^-4	UTR_3_PRIME CG6180 UPSTREAM CG15484 DOWNSTREAM CG5787 & 1 other INTRAGENIC CG6180 INTERGENIC
3R	19815983	3R_19815983_SNP [dm3] 3R_23990261_SNP [dm6]	T	C	1.763e^-9	3.253e^-4	SYNONYMOUS_CODING CG13604
2L	12708133	2L_12708133_SNP [dm3] 2L_12708133_SNP [dm6]	T	C	3.305e^-9	5.543e^-4	SYNONYMOUS_CODING CG6180 UPSTREAM CG15484 DOWNSTREAM CG5787	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
3R	9623873	3R_9623873_SNP [dm3] 3R_13798151_SNP [dm6]	T	G	6.667e^-9	0.001	DOWNSTREAM tRNA:CR31331 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	26174742	3R_26174742_SNP [dm3] 3R_30349020_SNP [dm6]	G	A	8.450e^-9	0.001	INTRON hdc
X	8914082	X_8914082_SNP [dm3] X_9020049_SNP [dm6]	T	C	8.766e^-9	0.001	INTRON CR43836 & 1 other
2R	13589085	2R_13589085_SNP [dm3] 2R_17701580_SNP [dm6]	G	A	1.071e^-8	0.001	UPSTREAM snoRNA:snR38:54Eb & 3 others DOWNSTREAM snoRNA:U76:54Eb & 3 others INTRON Uhg1
3R	17768831	3R_17768831_SNP [dm3] 3R_21943109_SNP [dm6]	A	T	1.316e^-8	0.001	INTERGENIC
3R	17768905	3R_17768905_SNP [dm3] 3R_21943183_SNP [dm6]	G	C	1.316e^-8	0.001	INTERGENIC
3R	25336829	3R_25336829_INS [dm3] 3R_29511107_INS [dm6]	T	TGT	1.316e^-8	0.001	INTERGENIC
3R	24644556	3R_24644556_SNP [dm3] 3R_28818834_SNP [dm6]	G	A	1.480e^-8	0.001	SYNONYMOUS_CODING CG1523	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	26550034	3R_26550034_SNP [dm3] 3R_30724312_SNP [dm6]	C	A	1.554e^-8	0.001	INTERGENIC
3R	13771597	3R_13771597_SNP [dm3] 3R_17945875_SNP [dm6]	G	T	2.274e^-8	0.002	INTRON cpo	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	25025473	3R_25025473_SNP [dm3] 3R_29199751_SNP [dm6]	C	T	2.480e^-8	0.002	UPSTREAM CG11899 DOWNSTREAM CG14515 INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	23398814	3R_23398814_INS [dm3] 3R_27573092_INS [dm6]	C	CAGC	2.688e^-8	0.002	INTRON wdb
2L	8139231	2L_8139231_SNP [dm3] 2L_8139231_SNP [dm6]	G	C	2.893e^-8	0.002	NON_SYNONYMOUS_CODING CG8552 UTR_5_PRIME CG8552	TF binding site mE1_TFBS_cad
3R	4954981	3R_4954981_SNP [dm3] 3R_9129259_SNP [dm6]	G	A	3.061e^-8	0.002	INTRON pum	TF binding site mE1_TFBS_Trl
X	21315818	X_21315818_SNP [dm3] X_21444791_SNP [dm6]	C	T	3.469e^-8	0.002	INTRON CG42343
3R	9624884	3R_9624884_SNP [dm3] 3R_13799162_SNP [dm6]	A	G	3.823e^-8	0.003	UPSTREAM tRNA:CR31331 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	13771513	3R_13771513_SNP [dm3] 3R_17945791_SNP [dm6]	G	A	4.103e^-8	0.003	INTRON cpo	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	6555947	2R_6555947_SNP [dm3] 2R_10668442_SNP [dm6]	A	T	4.267e^-8	0.003	INTERGENIC
2R	18155898	2R_18155898_SNP [dm3] 2R_22268393_SNP [dm6]	A	G	4.999e^-8	0.003	INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18882253	3L_18882253_SNP [dm3] 3L_18889153_SNP [dm6]	A	C	5.550e^-8	0.003	INTRON CG3961
3R	13961647	3R_13961647_SNP [dm3] 3R_18135925_SNP [dm6]	G	A	5.954e^-8	0.003	DOWNSTREAM sr INTERGENIC
3R	25338353	3R_25338353_SNP [dm3] 3R_29512631_SNP [dm6]	C	A	7.114e^-8	0.004	INTERGENIC
3L	938650	3L_938650_SNP [dm3] 3L_938650_SNP [dm6]	T	A	7.547e^-8	0.004	INTRON Glut1
3R	25191950	3R_25191950_SNP [dm3] 3R_29366228_SNP [dm6]	G	A	7.547e^-8	0.004	INTERGENIC
2R	17734815	2R_17734815_SNP [dm3] 2R_21847310_SNP [dm6]	C	G	8.226e^-8	0.004	INTERGENIC
2L	3940784	2L_3940784_SNP [dm3] 2L_3940784_SNP [dm6]	A	G	9.800e^-8	0.005	INTRON fred
2L	3940816	2L_3940816_SNP [dm3] 2L_3940816_SNP [dm6]	C	A	9.800e^-8	0.005	INTRON fred
X	2152633	X_2152633_SNP [dm3] X_2258600_SNP [dm6]	G	T	1.177e^-7	0.005	UTR_5_PRIME CG3078	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8334362	2L_8334362_SNP [dm3] 2L_8334362_SNP [dm6]	C	T	1.184e^-7	0.005	INTERGENIC
3R	25338315	3R_25338315_SNP [dm3] 3R_29512593_SNP [dm6]	G	T	1.191e^-7	0.005	INTERGENIC
2R	8904295	2R_8904295_SNP [dm3] 2R_13016790_SNP [dm6]	T	C	1.193e^-7	0.005	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	18887752	2R_18887752_INS [dm3] 2R_23000229_INS [dm6]	T	TAGT	1.242e^-7	0.005	INTRON twi
3L	1164380	3L_1164380_SNP [dm3] 3L_1164380_SNP [dm6]	A	G	1.322e^-7	0.006	INTRON bab2	regulatory region REDfly_CRMs
X	14910208	X_14910208_SNP [dm3] X_15016175_SNP [dm6]	T	C	1.550e^-7	0.006	SYNONYMOUS_CODING hiw	TF binding site mE1_TFBS_chinmo
X	14910319	X_14910319_SNP [dm3] X_15016286_SNP [dm6]	T	G	1.550e^-7	0.006	SYNONYMOUS_CODING hiw	TF binding site mE1_TFBS_chinmo
X	6622290	X_6622290_SNP [dm3] X_6728257_SNP [dm6]	G	A	1.819e^-7	0.007	INTRON CG3168	TF binding site BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
3R	25025282	3R_25025282_SNP [dm3] 3R_29199560_SNP [dm6]	G	T	1.849e^-7	0.007	UPSTREAM CG11899 DOWNSTREAM CG14515 INTERGENIC
2L	12333726	2L_12333726_INS [dm3] 2L_12333726_INS [dm6]	G	GTGTAATGTCCTTGAGCTGC...	1.904e^-7	0.007	INTERGENIC
2L	12444045	2L_12444045_SNP [dm3] 2L_12444045_SNP [dm6]	T	C	1.912e^-7	0.007	SYNONYMOUS_CODING Oatp33Ea	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	13771610	3R_13771610_DEL [dm3] 3R_17945888_DEL [dm6]	GACGGGG	G	1.925e^-7	0.007	INTRON cpo	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	8904164	2R_8904164_SNP [dm3] 2R_13016659_SNP [dm6]	T	A	2.482e^-7	0.009	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	8904174	2R_8904174_SNP [dm3] 2R_13016669_SNP [dm6]	A	T	2.482e^-7	0.009	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	17853263	3R_17853263_SNP [dm3] 3R_22027541_SNP [dm6]	C	A	2.545e^-7	0.009	UPSTREAM ND42 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	13790575	3L_13790575_SNP [dm3] 3L_13797475_SNP [dm6]	T	C	3.273e^-7	0.011	INTRON bru-3
X	13197213	X_13197213_SNP [dm3] X_13303180_SNP [dm6]	T	A	4.011e^-7	0.013	UPSTREAM CG1764 & 2 others INTERGENIC
2R	18156797	2R_18156797_SNP [dm3] 2R_22269292_SNP [dm6]	C	G	4.108e^-7	0.013	INTRON dve	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo
X	21203559	X_21203559_SNP [dm3] X_21332532_SNP [dm6]	G	A	4.304e^-7	0.014	DOWNSTREAM tty INTRON tty	transposable element FlyBase
2R	18792570	2R_18792570_SNP [dm3] 2R_22905047_SNP [dm6]	C	T	4.470e^-7	0.014	INTRON nahoda	TF binding site mE1_TFBS_HSA
3R	16220024	3R_16220024_SNP [dm3] 3R_20394302_SNP [dm6]	A	G	4.572e^-7	0.014	INTRON Gfrl
3R	25015299	3R_25015299_SNP [dm3] 3R_29189577_SNP [dm6]	G	A	4.923e^-7	0.015	INTRON CG14509
3L	18439241	3L_18439241_SNP [dm3] 3L_18446141_SNP [dm6]	T	A	5.421e^-7	0.016	INTERGENIC
3R	9979113	3R_9979113_SNP [dm3] 3R_14153391_SNP [dm6]	G	A	5.782e^-7	0.017	SYNONYMOUS_CODING CG9722 UPSTREAM CG42500 DOWNSTREAM CR44215
3R	24064267	3R_24064267_SNP [dm3] 3R_28238545_SNP [dm6]	C	G	6.078e^-7	0.017	UTR_3_PRIME CG34354 EXON CR45041
2R	18156244	2R_18156244_SNP [dm3] 2R_22268739_SNP [dm6]	T	C	6.122e^-7	0.017	INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	7737726	2R_7737726_SNP [dm3] 2R_11850221_SNP [dm6]	G	T	6.134e^-7	0.017	SYNONYMOUS_CODING Sln	TF binding site mE1_TFBS_chinmo
X	2213545	X_2213545_SNP [dm3] X_2319512_SNP [dm6]	A	C	6.259e^-7	0.017	INTRON phl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	16082409	3R_16082409_SNP [dm3] 3R_20256687_SNP [dm6]	A	C	6.448e^-7	0.017	INTRON cic
3R	19816028	3R_19816028_SNP [dm3] 3R_23990306_SNP [dm6]	G	A	6.452e^-7	0.017	SYNONYMOUS_CODING CG13604
2L	12708157	2L_12708157_SNP [dm3] 2L_12708157_SNP [dm6]	G	A	7.281e^-7	0.019	SYNONYMOUS_CODING CG6180 UPSTREAM CG15484 DOWNSTREAM CG5787	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
3L	957420	3L_957420_DEL [dm3] 3L_957420_DEL [dm6]	TGT	T	7.899e^-7	0.019	INTRON Glut1
3R	25338309	3R_25338309_SNP [dm3] 3R_29512587_SNP [dm6]	T	C	7.961e^-7	0.019	INTERGENIC
2L	11671460	2L_11671460_SNP [dm3] 2L_11671460_SNP [dm6]	G	T	8.127e^-7	0.019	INTERGENIC
2L	11671461	2L_11671461_SNP [dm3] 2L_11671461_SNP [dm6]	G	T	8.672e^-7	0.019	INTERGENIC
3R	17634903	3R_17634903_INS [dm3] 3R_21809181_INS [dm6]	A	AA	8.912e^-7	0.019	UPSTREAM CASK INTRON CASK	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	8139247	2L_8139247_SNP [dm3] 2L_8139247_SNP [dm6]	T	C	9.067e^-7	0.019	SYNONYMOUS_CODING CG8552 UTR_5_PRIME CG8552	TF binding site mE1_TFBS_cad
3R	26074512	3R_26074512_SNP [dm3] 3R_30248790_SNP [dm6]	C	G	9.084e^-7	0.019	UPSTREAM tRNA:CR31383 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
2R	13906946	2R_13906946_SNP [dm3] 2R_18019441_SNP [dm6]	C	T	9.587e^-7	0.019	SPLICE_SITE_REGION CG5084 SYNONYMOUS_CODING CG5084 UPSTREAM CG10910	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	15011381	2R_15011381_SNP [dm3] 2R_19123876_SNP [dm6]	C	A	9.587e^-7	0.019	SYNONYMOUS_CODING CG15117
2R	7722351	2R_7722351_SNP [dm3] 2R_11834846_SNP [dm6]	G	A	9.587e^-7	0.019	INTRON Sobp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	17647237	3R_17647237_SNP [dm3] 3R_21821515_SNP [dm6]	T	G	9.587e^-7	0.019	INTRON CASK	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
X	16707912	X_16707912_SNP [dm3] X_16813879_SNP [dm6]	T	A	9.587e^-7	0.019	INTRON CG4829
3R	9623864	3R_9623864_INS [dm3] 3R_13798142_INS [dm6]	A	AG	1.116e^-6	0.019	DOWNSTREAM tRNA:CR31331 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	25435612	3R_25435612_SNP [dm3] 3R_29609890_SNP [dm6]	A	T	1.145e^-6	0.019	INTRON alph	TF binding site mE1_TFBS_chinmo
X	2201307	X_2201307_DEL [dm3] X_2307274_DEL [dm6]	CTTATCC	C	1.203e^-6	0.019	INTRON phl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens mE1_TFBS_Trl
3R	19895580	3R_19895580_SNP [dm3] 3R_24069858_SNP [dm6]	G	A	1.274e^-6	0.019	INTRON 4EHP
2R	11282469	2R_11282469_SNP [dm3] 2R_15394964_SNP [dm6]	T	C	1.274e^-6	0.019	INTERGENIC
3L	937879	3L_937879_SNP [dm3] 3L_937879_SNP [dm6]	A	G	1.423e^-6	0.019	INTRON Glut1
3L	937880	3L_937880_SNP [dm3] 3L_937880_SNP [dm6]	G	A	1.423e^-6	0.019	INTRON Glut1
3R	11276511	3R_11276511_SNP [dm3] 3R_15450789_SNP [dm6]	C	T	1.435e^-6	0.019	INTRON AdamTS-A
2L	9517095	2L_9517095_SNP [dm3] 2L_9517095_SNP [dm6]	G	A	1.478e^-6	0.019	INTRON CG33298
2R	8903998	2R_8903998_SNP [dm3] 2R_13016493_SNP [dm6]	G	C	1.478e^-6	0.019	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	8904001	2R_8904001_SNP [dm3] 2R_13016496_SNP [dm6]	A	T	1.478e^-6	0.019	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	8904252	2R_8904252_INS [dm3] 2R_13016747_INS [dm6]	A	AACA	1.478e^-6	0.019	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	12777935	2R_12777935_SNP [dm3] 2R_16890430_SNP [dm6]	G	A	1.484e^-6	0.019	INTRON CG8910
2R	12779167	2R_12779167_SNP [dm3] 2R_16891662_SNP [dm6]	C	T	1.484e^-6	0.019	INTRON CG8910	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2L	11290588	2L_11290588_SNP [dm3] 2L_11290588_SNP [dm6]	T	C	1.484e^-6	0.019	DOWNSTREAM CR43409 INTERGENIC
2L	11290612	2L_11290612_SNP [dm3] 2L_11290612_SNP [dm6]	C	A	1.484e^-6	0.019	DOWNSTREAM CR43409 INTERGENIC
2L	11290625	2L_11290625_SNP [dm3] 2L_11290625_SNP [dm6]	T	C	1.484e^-6	0.019	DOWNSTREAM CR43409 INTERGENIC
2R	18868995	2R_18868995_SNP [dm3] 2R_22981472_SNP [dm6]	T	A	1.484e^-6	0.019	INTERGENIC

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By genomic position
Variant impact
Gene name

pc_MB_Beta_Thin phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results