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=5.179e^-10)
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

Covariate	p-value	Significance
wolba	0.01550
In_2L_t	0.08658
In_3R_P	0.02320

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	6.1156	0.047

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2523 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
X	12949111	X_12949111_SNP [dm3] X_13055078_SNP [dm6]	G	T	3.718e^-7	0.651	DOWNSTREAM CR44840 INTRON rad & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	2425914	2L_2425914_SNP [dm3] 2L_2425914_SNP [dm6]	A	G	1.159e^-6	0.651	DOWNSTREAM CG44139 INTERGENIC
3R	18743508	3R_18743508_SNP [dm3] 3R_22917786_SNP [dm6]	C	A	1.850e^-6	0.651	INTRON klg
3L	10745981	3L_10745981_SNP [dm3] 3L_10752881_SNP [dm6]	G	T	2.145e^-6	0.651	INTERGENIC
2L	8999883	2L_8999883_SNP [dm3] 2L_8999883_SNP [dm6]	T	G	3.296e^-6	0.651	DOWNSTREAM Try29F INTERGENIC
3L	884387	3L_884387_SNP [dm3] 3L_884387_SNP [dm6]	C	A	3.309e^-6	0.651	INTRON CG32479
3L	9579486	3L_9579486_SNP [dm3] 3L_9586386_SNP [dm6]	A	G	3.706e^-6	0.651	INTRON CG42673	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	9578638	3L_9578638_SNP [dm3] 3L_9585538_SNP [dm6]	A	T	3.750e^-6	0.651	INTRON CG42673
X	5176251	X_5176251_SNP [dm3] X_5282218_SNP [dm6]	A	T	4.165e^-6	0.651	INTERGENIC
3L	3178846	3L_3178846_SNP [dm3] 3L_3178846_SNP [dm6]	T	A	4.232e^-6	0.651	UPSTREAM Girdin & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
2L	8999866	2L_8999866_DEL [dm3] 2L_8999866_DEL [dm6]	AG	T	4.944e^-6	0.651	DOWNSTREAM Try29F INTERGENIC
3L	9579505	3L_9579505_SNP [dm3] 3L_9586405_SNP [dm6]	C	T	5.078e^-6	0.651	INTRON CG42673	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	7228237	2L_7228237_SNP [dm3] 2L_7228237_SNP [dm6]	T	A	6.565e^-6	0.651	NON_SYNONYMOUS_CODING CG43799 INTRON Ndae1
2L	10982552	2L_10982552_SNP [dm3] 2L_10982552_SNP [dm6]	A	G	7.182e^-6	0.651	UTR_3_PRIME piwi DOWNSTREAM SCAR
2L	8999898	2L_8999898_SNP [dm3] 2L_8999898_SNP [dm6]	C	A	7.251e^-6	0.651	DOWNSTREAM Try29F INTERGENIC
3L	16993476	3L_16993476_SNP [dm3] 3L_17000376_SNP [dm6]	T	C	7.345e^-6	0.651	INTRON CG3764
2R	5849707	2R_5849707_SNP [dm3] 2R_9962202_SNP [dm6]	A	G	7.723e^-6	0.651	INTRON Pal1	TF binding site mE1_TFBS_cad
2R	11101785	2R_11101785_INS [dm3] 2R_15214280_INS [dm6]	T	TT	7.740e^-6	0.651	UTR_3_PRIME CG8093 UPSTREAM row	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	9526702	3L_9526702_SNP [dm3] 3L_9533602_SNP [dm6]	G	A	7.861e^-6	0.651	INTERGENIC
3L	3178662	3L_3178662_SNP [dm3] 3L_3178662_SNP [dm6]	C	A	8.319e^-6	0.651	UPSTREAM Girdin & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
3L	8472669	3L_8472669_SNP [dm3] 3L_8479569_SNP [dm6]	C	A	8.332e^-6	0.651	SYNONYMOUS_CODING CG43163	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
X	19883202	X_19883202_SNP [dm3] X_19989169_SNP [dm6]	A	C	8.792e^-6	0.651	INTERGENIC
3L	3178812	3L_3178812_INS [dm3] 3L_3178812_INS [dm6]	G	AAAAAA	9.023e^-6	0.651	UPSTREAM Girdin & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
X	7718463	X_7718463_SNP [dm3] X_7824430_SNP [dm6]	G	A	9.437e^-6	0.651	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8999857	2L_8999857_SNP [dm3] 2L_8999857_SNP [dm6]	A	C	9.502e^-6	0.651	DOWNSTREAM Try29F INTERGENIC
2L	8999900	2L_8999900_SNP [dm3] 2L_8999900_SNP [dm6]	T	C	9.718e^-6	0.651	DOWNSTREAM Try29F INTERGENIC
X	21874197	X_21874197_DEL [dm3] X_22472361_DEL [dm6]	AA	A	1.018e^-5	0.651	UPSTREAM CG14613 INTERGENIC	TF binding site BDTNP1_TFBS_dl transposable element FlyBase
3L	3179317	3L_3179317_SNP [dm3] 3L_3179317_SNP [dm6]	C	T	1.048e^-5	0.651	UTR_5_PRIME Girdin UPSTREAM CG14964	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	9372721	3L_9372721_SNP [dm3] 3L_9379621_SNP [dm6]	C	T	1.080e^-5	0.651	UPSTREAM Hsp67Ba EXON CR43481	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	1438120	2L_1438120_SNP [dm3] 2L_1438120_SNP [dm6]	A	G	1.128e^-5	0.651	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_Kr
2L	10456662	2L_10456662_DEL [dm3] 2L_10456662_DEL [dm6]	GGGAAAAATGTTCTAGACCA...	G	1.134e^-5	0.651	UPSTREAM CG5322 & 1 other INTRON CG5322
X	3518956	X_3518956_SNP [dm3] X_3624923_SNP [dm6]	G	A	1.195e^-5	0.651	INTRON AstA-R1
2R	2869800	2R_2869800_SNP [dm3] 2R_6982295_SNP [dm6]	C	T	1.223e^-5	0.651	SYNONYMOUS_CODING CG30156 INTRON vimar	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	900190	2L_900190_SNP [dm3] 2L_900190_SNP [dm6]	A	C	1.296e^-5	0.651	NON_SYNONYMOUS_CODING Lsp1beta	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	21016515	3R_21016515_SNP [dm3] 3R_25190793_SNP [dm6]	C	T	1.300e^-5	0.651	SYNONYMOUS_CODING dan INTRON lobo	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3012750	2L_3012750_SNP [dm3] 2L_3012750_SNP [dm6]	C	T	1.354e^-5	0.651	INTRON CG17265	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	21939767	2L_21939767_SNP [dm3] 2L_21939767_SNP [dm6]	C	G	1.430e^-5	0.651	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	9705125	2R_9705125_SNP [dm3] 2R_13817620_SNP [dm6]	C	T	1.432e^-5	0.651	INTRON stj
3L	4013531	3L_4013531_SNP [dm3] 3L_4013531_SNP [dm6]	T	G	1.435e^-5	0.651	INTERGENIC
3L	8468934	3L_8468934_SNP [dm3] 3L_8475834_SNP [dm6]	T	A	1.436e^-5	0.651	NON_SYNONYMOUS_CODING CG43163	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	19534640	2R_19534640_SNP [dm3] 2R_23647117_SNP [dm6]	T	A	1.457e^-5	0.651	INTRON retn	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
X	12463256	X_12463256_SNP [dm3] X_12569223_SNP [dm6]	T	A	1.529e^-5	0.651	UTR_3_PRIME CG11138 UPSTREAM CG43921 DOWNSTREAM CG11138
2R	4454506	2R_4454506_SNP [dm3] 2R_8567001_SNP [dm6]	G	C	1.544e^-5	0.651	UTR_5_PRIME Cyp6a14
2R	2868456	2R_2868456_SNP [dm3] 2R_6980951_SNP [dm6]	G	T	1.558e^-5	0.651	DOWNSTREAM CR44170 & 1 other INTRON vimar EXON CR44171	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA
2R	14370664	2R_14370664_SNP [dm3] 2R_18483159_SNP [dm6]	T	C	1.651e^-5	0.651	INTRON CG30116
3L	7961614	3L_7961614_SNP [dm3] 3L_7968514_SNP [dm6]	G	A	1.686e^-5	0.651	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	11874812	3R_11874812_SNP [dm3] 3R_16049090_SNP [dm6]	A	T	1.690e^-5	0.651	UPSTREAM CG5013 INTRON ird5 EXON CR45212	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad
2R	13859845	2R_13859845_SNP [dm3] 2R_17972340_SNP [dm6]	C	G	1.700e^-5	0.651	INTERGENIC
3L	3179264	3L_3179264_SNP [dm3] 3L_3179264_SNP [dm6]	A	G	1.746e^-5	0.651	UTR_5_PRIME Girdin UPSTREAM CG14964	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	1079123	2L_1079123_SNP [dm3] 2L_1079123_SNP [dm6]	C	T	1.794e^-5	0.651	SPLICE_SITE_REGION ast SYNONYMOUS_CODING ast	TF binding site mE1_TFBS_sens
X	12949219	X_12949219_SNP [dm3] X_13055186_SNP [dm6]	T	C	1.839e^-5	0.651	NON_SYNONYMOUS_CODING CG12715 DOWNSTREAM CR44840 INTRON rad	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	2703887	X_2703887_DEL [dm3] X_2809854_DEL [dm6]	GG	G	1.925e^-5	0.651	UPSTREAM CG12498 INTRON kirre	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	14662671	2L_14662671_SNP [dm3] 2L_14662671_SNP [dm6]	T	A	1.935e^-5	0.651	INTRON osp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
X	7718460	X_7718460_SNP [dm3] X_7824427_SNP [dm6]	C	T	1.949e^-5	0.651	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	25610363	3R_25610363_SNP [dm3] 3R_29784641_SNP [dm6]	G	T	1.954e^-5	0.651	INTRON kay
3R	20980505	3R_20980505_SNP [dm3] 3R_25154783_SNP [dm6]	G	A	1.972e^-5	0.651	INTERGENIC
2L	2435363	2L_2435363_SNP [dm3] 2L_2435363_SNP [dm6]	G	A	1.979e^-5	0.651	INTRON dpp	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA
3L	3180439	3L_3180439_SNP [dm3] 3L_3180439_SNP [dm6]	T	C	2.206e^-5	0.687	SYNONYMOUS_CODING Girdin	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	8999903	2L_8999903_SNP [dm3] 2L_8999903_SNP [dm6]	G	A	2.276e^-5	0.687	DOWNSTREAM Try29F INTERGENIC
2R	9349307	2R_9349307_SNP [dm3] 2R_13461802_SNP [dm6]	C	T	2.381e^-5	0.687	INTRON arr	TF binding site mE1_TFBS_chinmo
3R	13928241	3R_13928241_SNP [dm3] 3R_18102519_SNP [dm6]	T	C	2.395e^-5	0.687	INTRON sr
X	14550487	X_14550487_SNP [dm3] X_14656454_SNP [dm6]	A	C	2.406e^-5	0.687	INTERGENIC
3L	14069263	3L_14069263_SNP [dm3] 3L_14076163_SNP [dm6]	T	C	2.420e^-5	0.687	UPSTREAM btl DOWNSTREAM Pex1 INTRON btl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	13376701	2L_13376701_SNP [dm3] 2L_13376701_SNP [dm6]	T	G	2.442e^-5	0.687	UTR_3_PRIME CG9302 DOWNSTREAM CG6565
2L	13431312	2L_13431312_SNP [dm3] 2L_13431312_SNP [dm6]	T	C	2.451e^-5	0.687	INTRON CG42784
2L	1436380	2L_1436380_SNP [dm3] 2L_1436380_SNP [dm6]	C	T	2.474e^-5	0.687	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	12333476	2R_12333476_SNP [dm3] 2R_16445971_SNP [dm6]	A	G	2.478e^-5	0.687	UPSTREAM CG15925 INTERGENIC
2R	865972	2R_865972_SNP [dm3] 2R_4978467_SNP [dm6]	C	G	2.490e^-5	0.687	INTRON Ir41a
3R	5156249	3R_5156249_SNP [dm3] 3R_9330527_SNP [dm6]	A	G	2.661e^-5	0.695	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
2R	6152623	2R_6152623_SNP [dm3] 2R_10265118_SNP [dm6]	C	T	2.724e^-5	0.695	UTR_5_PRIME CG12910 UPSTREAM CG12910	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	11874732	3R_11874732_SNP [dm3] 3R_16049010_SNP [dm6]	A	G	2.766e^-5	0.695	UPSTREAM CG5013 DOWNSTREAM CR45212 INTRON ird5	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	7961585	3L_7961585_SNP [dm3] 3L_7968485_SNP [dm6]	C	A	2.897e^-5	0.695	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	880090	2L_880090_SNP [dm3] 2L_880090_SNP [dm6]	A	G	2.905e^-5	0.695	SYNONYMOUS_CODING CG15824	TF binding site mE1_TFBS_cad
X	8769077	X_8769077_SNP [dm3] X_8875044_SNP [dm6]	C	T	2.924e^-5	0.695	INTRON Moe	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	2025383	2L_2025383_SNP [dm3] 2L_2025383_SNP [dm6]	G	C	2.981e^-5	0.695	INTRON CG4238
3L	12674677	3L_12674677_SNP [dm3] 3L_12681577_SNP [dm6]	T	G	3.071e^-5	0.695	INTERGENIC
2R	8949103	2R_8949103_SNP [dm3] 2R_13061598_SNP [dm6]	T	C	3.074e^-5	0.695	INTRON Drl-2
2L	14662688	2L_14662688_SNP [dm3] 2L_14662688_SNP [dm6]	T	C	3.075e^-5	0.695	INTRON osp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	8980845	2L_8980845_SNP [dm3] 2L_8980845_SNP [dm6]	G	A	3.082e^-5	0.695	INTRON CG13101 & 1 other
X	12170120	X_12170120_SNP [dm3] X_12276087_SNP [dm6]	A	G	3.123e^-5	0.695	DOWNSTREAM CG45603 INTRON Ten-a
2L	10455715	2L_10455715_SNP [dm3] 2L_10455715_SNP [dm6]	G	A	3.232e^-5	0.695	SYNONYMOUS_CODING CG5322	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	2874589	2R_2874589_SNP [dm3] 2R_6987084_SNP [dm6]	G	T	3.518e^-5	0.695	INTRON CG17002	TF binding site mE1_TFBS_cad
3R	5156291	3R_5156291_SNP [dm3] 3R_9330569_SNP [dm6]	T	C	3.540e^-5	0.695	UPSTREAM CG12951 DOWNSTREAM CG16749 INTERGENIC
3R	25784573	3R_25784573_SNP [dm3] 3R_29958851_SNP [dm6]	C	T	3.576e^-5	0.695	INTRON TkR99D
3L	2518216	3L_2518216_SNP [dm3] 3L_2518216_SNP [dm6]	A	T	3.672e^-5	0.695	INTRON Spn & 1 other
X	4620997	X_4620997_SNP [dm3] X_4726964_SNP [dm6]	A	G	3.830e^-5	0.695	NON_SYNONYMOUS_CODING Proc-R
3R	26079337	3R_26079337_SNP [dm3] 3R_30253615_SNP [dm6]	C	T	3.852e^-5	0.695	DOWNSTREAM CG9682 INTRON CG18404
2R	9705497	2R_9705497_SNP [dm3] 2R_13817992_SNP [dm6]	G	A	3.864e^-5	0.695	UTR_3_PRIME stj
3L	8080844	3L_8080844_SNP [dm3] 3L_8087744_SNP [dm6]	C	T	3.907e^-5	0.695	UTR_3_PRIME CG7565 INTRON Ect4
3L	4783084	3L_4783084_SNP [dm3] 3L_4783084_SNP [dm6]	A	T	3.909e^-5	0.695	INTRON RhoGEF64C
2L	2435366	2L_2435366_DEL [dm3] 2L_2435366_DEL [dm6]	ACTTGTA	A	4.023e^-5	0.695	INTRON dpp	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA
3R	20980559	3R_20980559_DEL [dm3] 3R_25154837_DEL [dm6]	AA	C	4.174e^-5	0.695	INTERGENIC
2L	2435985	2L_2435985_SNP [dm3] 2L_2435985_SNP [dm6]	T	A	4.214e^-5	0.695	INTRON dpp	TF binding site mE1_TFBS_cnc
X	21282426	X_21282426_SNP [dm3] X_21411399_SNP [dm6]	G	A	4.238e^-5	0.695	UPSTREAM CR45003 INTERGENIC
2L	14662665	2L_14662665_SNP [dm3] 2L_14662665_SNP [dm6]	T	C	4.239e^-5	0.695	INTRON osp	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	916144	2L_916144_SNP [dm3] 2L_916144_SNP [dm6]	C	T	4.263e^-5	0.695	SYNONYMOUS_CODING GluRIIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_inv
2R	8964882	2R_8964882_SNP [dm3] 2R_13077377_SNP [dm6]	G	A	4.298e^-5	0.695	INTRON Drl-2	TF binding site mE1_TFBS_cad
3L	5474338	3L_5474338_SNP [dm3] 3L_5481238_SNP [dm6]	A	G	4.534e^-5	0.695	NON_SYNONYMOUS_CODING CG4835
2L	3200459	2L_3200459_SNP [dm3] 2L_3200459_SNP [dm6]	A	G	4.553e^-5	0.695	UPSTREAM CG34393 INTRON CG34393
3R	9722988	3R_9722988_SNP [dm3] 3R_13897266_SNP [dm6]	C	T	4.732e^-5	0.695	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

Canton S(B)/DGRP phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results