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=5.021e^-9)
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

Covariate	χ²	p-value	Significance
In_2R_NS	6.6271	0.0364

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3598 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
2L	1103817	2L_1103817_SNP [dm3] 2L_1103817_SNP [dm6]	G	A	1.006e^-7	0.189	SYNONYMOUS_CODING mtRNApol	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	2969875	3R_2969875_SNP [dm3] 3R_7144153_SNP [dm6]	A	G	3.771e^-7	0.194	NON_SYNONYMOUS_CODING CG14610 UPSTREAM CG2656 EXON CR42738
X	8901926	X_8901926_SNP [dm3] X_9007893_SNP [dm6]	T	C	5.119e^-7	0.194	INTRON rdgA & 1 other
2L	6863604	2L_6863604_SNP [dm3] 2L_6863604_SNP [dm6]	A	T	5.235e^-7	0.194	INTRON Nha1
3L	19428254	3L_19428254_SNP [dm3] 3L_19435154_SNP [dm6]	C	A	5.540e^-7	0.194	INTERGENIC
2L	1470621	2L_1470621_SNP [dm3] 2L_1470621_SNP [dm6]	C	T	6.192e^-7	0.194	INTERGENIC
2R	17166739	2R_17166739_SNP [dm3] 2R_21279234_SNP [dm6]	G	C	9.069e^-7	0.209	INTRON Rgk3
3R	2868457	3R_2868457_SNP [dm3] 3R_7042735_SNP [dm6]	A	T	1.034e^-6	0.209	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	12154049	2L_12154049_SNP [dm3] 2L_12154049_SNP [dm6]	A	T	1.291e^-6	0.209	INTRON CG31760
2L	12571601	2L_12571601_SNP [dm3] 2L_12571601_SNP [dm6]	G	A	1.392e^-6	0.209	UPSTREAM CR44598 EXON CR44597
2L	3560264	2L_3560264_DEL [dm3] 2L_3560264_DEL [dm6]	GGC	G	1.455e^-6	0.209	INTERGENIC
2R	12295309	2R_12295309_SNP [dm3] 2R_16407804_SNP [dm6]	A	C	1.570e^-6	0.209	INTRON Sema-2b
3L	18290740	3L_18290740_SNP [dm3] 3L_18297640_SNP [dm6]	G	A	1.736e^-6	0.209	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	2672894	3R_2672894_SNP [dm3] 3R_6847172_SNP [dm6]	C	A	1.800e^-6	0.209	INTRON Scr	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	1103753	2L_1103753_SNP [dm3] 2L_1103753_SNP [dm6]	T	G	1.859e^-6	0.209	NON_SYNONYMOUS_CODING mtRNApol	TF binding site mE1_TFBS_cad
3R	23990720	3R_23990720_SNP [dm3] 3R_28164998_SNP [dm6]	A	T	2.075e^-6	0.209	INTRON CG34354
3R	2906048	3R_2906048_SNP [dm3] 3R_7080326_SNP [dm6]	G	A	2.144e^-6	0.209	UTR_5_PRIME Ref1	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	1363548	3L_1363548_SNP [dm3] 3L_1363548_SNP [dm6]	C	T	2.550e^-6	0.209	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	6626787	3L_6626787_SNP [dm3] 3L_6633687_SNP [dm6]	C	T	2.602e^-6	0.209	SYNONYMOUS_CODING GluRIA
2L	14242888	2L_14242888_SNP [dm3] 2L_14242888_SNP [dm6]	T	C	3.060e^-6	0.209	INTERGENIC
2L	14242889	2L_14242889_SNP [dm3] 2L_14242889_SNP [dm6]	T	A	3.060e^-6	0.209	INTERGENIC
3R	23066252	3R_23066252_SNP [dm3] 3R_27240530_SNP [dm6]	C	T	3.138e^-6	0.209	SYNONYMOUS_CODING DNApol-alpha73 UPSTREAM CG17991	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	6863562	2L_6863562_SNP [dm3] 2L_6863562_SNP [dm6]	C	A	3.169e^-6	0.209	INTRON Nha1
2L	13916332	2L_13916332_SNP [dm3] 2L_13916332_SNP [dm6]	A	T	3.214e^-6	0.209	INTRON Ance-3	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23990716	3R_23990716_SNP [dm3] 3R_28164994_SNP [dm6]	C	A	3.340e^-6	0.209	INTRON CG34354
2L	14242877	2L_14242877_SNP [dm3] 2L_14242877_SNP [dm6]	T	G	3.524e^-6	0.209	INTERGENIC
2R	19629168	2R_19629168_SNP [dm3] 2R_23741645_SNP [dm6]	A	G	3.550e^-6	0.209	INTRON egl
2L	14242878	2L_14242878_SNP [dm3] 2L_14242878_SNP [dm6]	A	T	3.710e^-6	0.209	INTERGENIC
2L	8582642	2L_8582642_SNP [dm3] 2L_8582642_SNP [dm6]	G	T	3.833e^-6	0.209	INTRON Sema-1a
2L	8582651	2L_8582651_SNP [dm3] 2L_8582651_SNP [dm6]	A	T	3.833e^-6	0.209	INTRON Sema-1a
3R	23990730	3R_23990730_SNP [dm3] 3R_28165008_SNP [dm6]	T	A	4.013e^-6	0.209	INTRON CG34354
2L	13916322	2L_13916322_SNP [dm3] 2L_13916322_SNP [dm6]	A	T	4.145e^-6	0.209	INTRON Ance-3	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	2351327	3L_2351327_SNP [dm3] 3L_2351327_SNP [dm6]	T	G	4.153e^-6	0.209	INTERGENIC
3R	2931095	3R_2931095_DEL [dm3] 3R_7105373_DEL [dm6]	CGCGCTTACCAATTAAAATA...	C	4.222e^-6	0.209	INTRON Alh	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	8582659	2L_8582659_SNP [dm3] 2L_8582659_SNP [dm6]	C	T	4.261e^-6	0.209	INTRON Sema-1a
3R	23990747	3R_23990747_SNP [dm3] 3R_28165025_SNP [dm6]	G	T	4.417e^-6	0.209	INTRON CG34354
3L	6041669	3L_6041669_SNP [dm3] 3L_6048569_SNP [dm6]	G	T	4.426e^-6	0.209	INTERGENIC
2L	14242881	2L_14242881_DEL [dm3] 2L_14242881_DEL [dm6]	AGCA	A	4.462e^-6	0.209	INTERGENIC
3R	23990804	3R_23990804_SNP [dm3] 3R_28165082_SNP [dm6]	T	C	4.568e^-6	0.209	INTRON CG34354
3R	15630508	3R_15630508_SNP [dm3] 3R_19804786_SNP [dm6]	G	A	4.575e^-6	0.209	INTRON bnl	TF binding site BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1620055	2L_1620055_SNP [dm3] 2L_1620055_SNP [dm6]	C	T	4.676e^-6	0.209	EXON CR44603
2R	11948886	2R_11948886_SNP [dm3] 2R_16061381_SNP [dm6]	T	C	4.819e^-6	0.209	DOWNSTREAM CG8405 INTERGENIC
2L	12154047	2L_12154047_SNP [dm3] 2L_12154047_SNP [dm6]	A	T	4.845e^-6	0.209	INTRON CG31760
2L	2121424	2L_2121424_SNP [dm3] 2L_2121424_SNP [dm6]	A	C	5.065e^-6	0.209	INTERGENIC
3L	16006440	3L_16006440_SNP [dm3] 3L_16013340_SNP [dm6]	T	A	5.113e^-6	0.209	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
3R	22573087	3R_22573087_SNP [dm3] 3R_26747365_SNP [dm6]	G	A	5.134e^-6	0.209	INTERGENIC
3L	19322258	3L_19322258_SNP [dm3] 3L_19329158_SNP [dm6]	T	C	5.673e^-6	0.216	INTRON pip
2L	12498223	2L_12498223_SNP [dm3] 2L_12498223_SNP [dm6]	G	A	5.729e^-6	0.216	UPSTREAM t-cup INTRON bun
3R	10779777	3R_10779777_SNP [dm3] 3R_14954055_SNP [dm6]	C	A	6.287e^-6	0.216	INTERGENIC
3L	8164869	3L_8164869_SNP [dm3] 3L_8171769_SNP [dm6]	C	T	6.324e^-6	0.216	SYNONYMOUS_CODING RecQ4	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	6041636	3L_6041636_SNP [dm3] 3L_6048536_SNP [dm6]	A	T	6.343e^-6	0.216	INTERGENIC
3R	23990732	3R_23990732_SNP [dm3] 3R_28165010_SNP [dm6]	A	G	6.346e^-6	0.216	INTRON CG34354
3L	8164773	3L_8164773_SNP [dm3] 3L_8171673_SNP [dm6]	A	G	6.541e^-6	0.216	SPLICE_SITE_REGION RecQ4 INTRON RecQ4	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	12154030	2L_12154030_INS [dm3] 2L_12154030_INS [dm6]	A	AT	6.893e^-6	0.216	INTRON CG31760
2L	13916316	2L_13916316_SNP [dm3] 2L_13916316_SNP [dm6]	C	T	6.923e^-6	0.216	INTRON Ance-3	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	13916320	2L_13916320_SNP [dm3] 2L_13916320_SNP [dm6]	G	A	6.923e^-6	0.216	INTRON Ance-3	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	16006442	3L_16006442_INS [dm3] 3L_16013342_INS [dm6]	C	TT	6.939e^-6	0.216	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
2L	14242892	2L_14242892_SNP [dm3] 2L_14242892_SNP [dm6]	T	C	7.326e^-6	0.216	INTERGENIC
3R	3085446	3R_3085446_DEL [dm3] 3R_7259724_DEL [dm6]	ATTGTCTTCGTT...	A	7.513e^-6	0.216	INTRON Gld
3L	1363638	3L_1363638_SNP [dm3] 3L_1363638_SNP [dm6]	A	T	7.560e^-6	0.216	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	13040943	3L_13040943_SNP [dm3] 3L_13047843_SNP [dm6]	A	G	7.576e^-6	0.216	UTR_3_PRIME CG11279 DOWNSTREAM Syx13 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14242896	2L_14242896_SNP [dm3] 2L_14242896_SNP [dm6]	T	A	7.596e^-6	0.216	INTERGENIC
2L	14242898	2L_14242898_DEL [dm3] 2L_14242898_DEL [dm6]	GT	G	7.622e^-6	0.216	INTERGENIC
2L	14242914	2L_14242914_SNP [dm3] 2L_14242914_SNP [dm6]	A	T	7.921e^-6	0.216	INTERGENIC
2L	14242919	2L_14242919_DEL [dm3] 2L_14242919_DEL [dm6]	TGG	T	7.921e^-6	0.216	INTERGENIC
2L	14242891	2L_14242891_SNP [dm3] 2L_14242891_SNP [dm6]	T	G	7.973e^-6	0.216	INTERGENIC
3R	23730086	3R_23730086_SNP [dm3] 3R_27904364_SNP [dm6]	A	G	8.105e^-6	0.216	INTRON CG34353
2L	14242894	2L_14242894_SNP [dm3] 2L_14242894_SNP [dm6]	A	C	8.404e^-6	0.216	INTERGENIC
3R	7233525	3R_7233525_SNP [dm3] 3R_11407803_SNP [dm6]	A	G	8.803e^-6	0.216	UPSTREAM mRpL40 DOWNSTREAM pros & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	14242903	2L_14242903_MNP [dm3] 2L_14242903_MNP [dm6]	CAC	TTG	8.812e^-6	0.216	INTERGENIC
2L	10503769	2L_10503769_SNP [dm3] 2L_10503769_SNP [dm6]	C	T	8.840e^-6	0.216	INTRON Myo31DF
2L	13916329	2L_13916329_SNP [dm3] 2L_13916329_SNP [dm6]	A	T	9.151e^-6	0.216	INTRON Ance-3	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6041633	3L_6041633_SNP [dm3] 3L_6048533_SNP [dm6]	C	T	9.162e^-6	0.216	INTERGENIC
3L	8176943	3L_8176943_SNP [dm3] 3L_8183843_SNP [dm6]	G	A	9.185e^-6	0.216	SYNONYMOUS_CODING ERR DOWNSTREAM CG7979	TF binding site mE1_TFBS_sens
2L	14242909	2L_14242909_MNP [dm3] 2L_14242909_MNP [dm6]	CCA	AGC	9.343e^-6	0.216	INTERGENIC
3R	2682554	3R_2682554_SNP [dm3] 3R_6856832_SNP [dm6]	A	C	9.409e^-6	0.216	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA transposable element FlyBase
2L	12498235	2L_12498235_SNP [dm3] 2L_12498235_SNP [dm6]	A	G	9.536e^-6	0.216	UPSTREAM t-cup INTRON bun
2L	14242907	2L_14242907_SNP [dm3] 2L_14242907_SNP [dm6]	T	C	9.639e^-6	0.216	INTERGENIC
3R	2682635	3R_2682635_SNP [dm3] 3R_6856913_SNP [dm6]	G	A	9.733e^-6	0.216	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	23305993	3R_23305993_SNP [dm3] 3R_27480271_SNP [dm6]	G	A	9.820e^-6	0.216	SYNONYMOUS_CODING Cyp6a18
2L	13734815	2L_13734815_SNP [dm3] 2L_13734815_SNP [dm6]	G	A	9.878e^-6	0.216	INTERGENIC
3L	3657270	3L_3657270_SNP [dm3] 3L_3657270_SNP [dm6]	G	C	9.985e^-6	0.216	INTERGENIC
2L	14242934	2L_14242934_SNP [dm3] 2L_14242934_SNP [dm6]	A	T	9.990e^-6	0.216	INTERGENIC
2L	14242923	2L_14242923_MNP [dm3] 2L_14242923_MNP [dm6]	ACACA	TATTT	1.011e^-5	0.216	INTERGENIC
3R	23065985	3R_23065985_SNP [dm3] 3R_27240263_SNP [dm6]	C	T	1.021e^-5	0.216	SYNONYMOUS_CODING DNApol-alpha73	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	1686494	2L_1686494_SNP [dm3] 2L_1686494_SNP [dm6]	C	T	1.039e^-5	0.216	INTRON chinmo
X	12702051	X_12702051_SNP [dm3] X_12808018_SNP [dm6]	T	C	1.053e^-5	0.216	INTRON Pde9
X	9003668	X_9003668_SNP [dm3] X_9109635_SNP [dm6]	G	C	1.058e^-5	0.216	START_GAINED AP-1gamma UTR_5_PRIME AP-1gamma INTRON AP-1gamma	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Ubx
X	14160242	X_14160242_SNP [dm3] X_14266209_SNP [dm6]	A	G	1.077e^-5	0.216	UTR_5_PRIME CG13404 UPSTREAM na DOWNSTREAM CG1461	TF binding site mE1_TFBS_chinmo
2L	12154033	2L_12154033_SNP [dm3] 2L_12154033_SNP [dm6]	C	T	1.085e^-5	0.216	INTRON CG31760
2L	12154035	2L_12154035_SNP [dm3] 2L_12154035_SNP [dm6]	C	T	1.085e^-5	0.216	INTRON CG31760
2L	12154039	2L_12154039_INS [dm3] 2L_12154039_INS [dm6]	T	AGTAC	1.085e^-5	0.216	INTRON CG31760
2L	12154044	2L_12154044_SNP [dm3] 2L_12154044_SNP [dm6]	C	A	1.085e^-5	0.216	INTRON CG31760
2L	12154045	2L_12154045_SNP [dm3] 2L_12154045_SNP [dm6]	C	T	1.085e^-5	0.216	INTRON CG31760
X	3085776	X_3085776_SNP [dm3] X_3191743_SNP [dm6]	C	G	1.094e^-5	0.216	INTRON dnc	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
3R	7240052	3R_7240052_SNP [dm3] 3R_11414330_SNP [dm6]	A	G	1.144e^-5	0.22	SYNONYMOUS_CODING Ranbp9	TF binding site mE1_TFBS_cad
2L	2225660	2L_2225660_SNP [dm3] 2L_2225660_SNP [dm6]	T	A	1.150e^-5	0.22	UTR_3_PRIME CG15387 UPSTREAM rti DOWNSTREAM papi	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	5317347	3L_5317347_SNP [dm3] 3L_5324247_SNP [dm6]	A	C	1.151e^-5	0.22	INTERGENIC
3L	16096641	3L_16096641_SNP [dm3] 3L_16103541_SNP [dm6]	T	G	1.160e^-5	0.22	SYNONYMOUS_CODING IntS9 DOWNSTREAM CG5414
2L	3741998	2L_3741998_SNP [dm3] 2L_3741998_SNP [dm6]	T	A	1.175e^-5	0.22	INTRON CG10019

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By genomic position
Variant impact
Gene name

neurBG2391/DGRP phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results