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=6.642e^-11)
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_2L_t	4.8646	0.0878

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2790 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	7710536	3R_7710536_SNP [dm3] 3R_11884814_SNP [dm6]	G	T	4.297e^-7	0.474	SYNONYMOUS_CODING mthl5 INTRON CG31368
2R	17085774	2R_17085774_SNP [dm3] 2R_21198269_SNP [dm6]	C	G	1.226e^-6	0.474	NON_SYNONYMOUS_CODING Lapsyn
3L	12641483	3L_12641483_SNP [dm3] 3L_12648383_SNP [dm6]	G	C	1.792e^-6	0.474	DOWNSTREAM CR43431 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	9180908	3L_9180908_SNP [dm3] 3L_9187808_SNP [dm6]	C	A	2.106e^-6	0.474	INTERGENIC
3R	20661325	3R_20661325_SNP [dm3] 3R_24835603_SNP [dm6]	C	A	2.269e^-6	0.474	UPSTREAM CR45216 & 1 other INTRON sosie	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2L	10232262	2L_10232262_DEL [dm3] 2L_10232262_DEL [dm6]	GA	G	2.387e^-6	0.474	UPSTREAM eEF1delta & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Ubx
2L	10232265	2L_10232265_SNP [dm3] 2L_10232265_SNP [dm6]	A	G	2.387e^-6	0.474	UPSTREAM eEF1delta & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Ubx
2L	10232271	2L_10232271_SNP [dm3] 2L_10232271_SNP [dm6]	C	A	2.497e^-6	0.474	UPSTREAM eEF1delta & 1 other INTERGENIC	insulator Insulator_Class_I.mE01 TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Ubx
X	4719972	X_4719972_SNP [dm3] X_4825939_SNP [dm6]	T	C	2.512e^-6	0.474	UPSTREAM CG12682 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	7709869	3R_7709869_SNP [dm3] 3R_11884147_SNP [dm6]	C	A	2.528e^-6	0.474	SYNONYMOUS_CODING mthl5 INTRON CG31368
3R	797524	3R_797524_SNP [dm3] 3R_4971802_SNP [dm6]	G	A	2.890e^-6	0.493	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_GATAe
3R	27281690	3R_27281690_SNP [dm3] 3R_31455968_SNP [dm6]	C	A	3.382e^-6	0.511	INTRON Gprk2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	22557224	3L_22557224_SNP [dm3] 3L_22564124_SNP [dm6]	C	A	3.543e^-6	0.511	INTERGENIC
2R	17098670	2R_17098670_SNP [dm3] 2R_21211165_SNP [dm6]	A	G	3.896e^-6	0.522	UTR_5_PRIME CG44245 DOWNSTREAM Glycogenin INTRON CG44245
3R	26642265	3R_26642265_DEL [dm3] 3R_30816543_DEL [dm6]	ATATAAAAACTGAGTCA...	A	4.650e^-6	0.532	INTRON cindr
X	18926968	X_18926968_SNP [dm3] X_19032935_SNP [dm6]	A	G	4.868e^-6	0.532	INTERGENIC
3R	20334443	3R_20334443_SNP [dm3] 3R_24508721_SNP [dm6]	T	G	5.096e^-6	0.532	DOWNSTREAM nAChRbeta2 INTERGENIC
2R	9525958	2R_9525958_SNP [dm3] 2R_13638453_SNP [dm6]	G	C	5.107e^-6	0.532	INTRON fas	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	19206622	3R_19206622_SNP [dm3] 3R_23380900_SNP [dm6]	G	A	5.725e^-6	0.539	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_chinmo
3L	15114583	3L_15114583_SNP [dm3] 3L_15121483_SNP [dm6]	C	G	5.751e^-6	0.539	UPSTREAM CG32847 INTRON Cep135 & 1 other	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10586705	2L_10586705_SNP [dm3] 2L_10586705_SNP [dm6]	T	C	6.124e^-6	0.547	INTRON Trim9	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	24051986	3R_24051986_SNP [dm3] 3R_28226264_SNP [dm6]	C	T	6.502e^-6	0.547	INTRON CG34354	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10060843	2R_10060843_SNP [dm3] 2R_14173338_SNP [dm6]	T	G	6.947e^-6	0.547	UPSTREAM cg DOWNSTREAM CG8331 INTRON mRpS16	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2R	7005107	2R_7005107_SNP [dm3] 2R_11117602_SNP [dm6]	C	T	7.313e^-6	0.547	UTR_3_PRIME Cyp12d1-p
3R	9917481	3R_9917481_SNP [dm3] 3R_14091759_SNP [dm6]	T	C	7.364e^-6	0.547	DOWNSTREAM CCHa1 INTRON Npc2b
2L	10232267	2L_10232267_SNP [dm3] 2L_10232267_SNP [dm6]	C	T	8.033e^-6	0.547	UPSTREAM eEF1delta & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Ubx
3R	6254419	3R_6254419_SNP [dm3] 3R_10428697_SNP [dm6]	C	T	8.446e^-6	0.547	INTERGENIC
2R	10060829	2R_10060829_SNP [dm3] 2R_14173324_SNP [dm6]	A	T	8.714e^-6	0.547	UPSTREAM cg DOWNSTREAM CG8331 INTRON mRpS16	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
X	17891135	X_17891135_SNP [dm3] X_17997102_SNP [dm6]	G	A	8.846e^-6	0.547	INTRON Sh
3R	19020819	3R_19020819_SNP [dm3] 3R_23195097_SNP [dm6]	A	T	1.052e^-5	0.547	INTRON cnc	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	24137495	3R_24137495_SNP [dm3] 3R_28311773_SNP [dm6]	G	A	1.086e^-5	0.547	INTERGENIC
3R	15008179	3R_15008179_SNP [dm3] 3R_19182457_SNP [dm6]	G	T	1.141e^-5	0.547	INTRON CG31475
2R	10460322	2R_10460322_SNP [dm3] 2R_14572817_SNP [dm6]	C	A	1.150e^-5	0.547	SYNONYMOUS_CODING LamC INTRON ttv
3L	3665857	3L_3665857_SNP [dm3] 3L_3665857_SNP [dm6]	G	A	1.190e^-5	0.547	INTERGENIC
3L	13080624	3L_13080624_SNP [dm3] 3L_13087524_SNP [dm6]	A	G	1.194e^-5	0.547	UPSTREAM CG17300 EXON CR45749
3R	27150894	3R_27150894_SNP [dm3] 3R_31325172_SNP [dm6]	A	G	1.233e^-5	0.547	INTRON CG34347
3R	15008064	3R_15008064_SNP [dm3] 3R_19182342_SNP [dm6]	T	A	1.264e^-5	0.547	INTRON CG31475
2L	489500	2L_489500_SNP [dm3] 2L_489500_SNP [dm6]	C	T	1.266e^-5	0.547	INTRON ush
3R	27153377	3R_27153377_SNP [dm3] 3R_31327655_SNP [dm6]	C	G	1.283e^-5	0.547	INTRON CG34347	TF binding site mE1_TFBS_cad
3R	20661315	3R_20661315_INS [dm3] 3R_24835593_INS [dm6]	A	ATACACA	1.433e^-5	0.547	UPSTREAM CR45216 & 1 other INTRON sosie	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3L	15600705	3L_15600705_SNP [dm3] 3L_15607605_SNP [dm6]	C	A	1.450e^-5	0.547	UTR_3_PRIME RhoGAP71E
X	17907798	X_17907798_SNP [dm3] X_18013765_SNP [dm6]	A	G	1.660e^-5	0.547	INTRON Sh
2R	10060925	2R_10060925_SNP [dm3] 2R_14173420_SNP [dm6]	G	A	1.678e^-5	0.547	SYNONYMOUS_CODING mRpS16 UPSTREAM cg DOWNSTREAM CG8331	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3R	25946483	3R_25946483_SNP [dm3] 3R_30120761_SNP [dm6]	T	A	1.688e^-5	0.547	UTR_3_PRIME sima	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	19739950	3R_19739950_SNP [dm3] 3R_23914228_SNP [dm6]	G	C	1.695e^-5	0.547	INTRON sba	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
3R	24181822	3R_24181822_SNP [dm3] 3R_28356100_SNP [dm6]	T	A	1.711e^-5	0.547	INTERGENIC
3R	20400124	3R_20400124_SNP [dm3] 3R_24574402_SNP [dm6]	T	A	1.718e^-5	0.547	INTRON CG13624
3R	21518257	3R_21518257_SNP [dm3] 3R_25692535_SNP [dm6]	T	G	1.733e^-5	0.547	INTERGENIC
X	7451414	X_7451414_SNP [dm3] X_7557381_SNP [dm6]	C	T	1.742e^-5	0.547	EXON CR44501	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	24134908	3R_24134908_SNP [dm3] 3R_28309186_SNP [dm6]	A	C	1.773e^-5	0.547	INTERGENIC
X	13402551	X_13402551_SNP [dm3] X_13508518_SNP [dm6]	C	T	1.801e^-5	0.547	INTRON Neto
2R	16956262	2R_16956262_SNP [dm3] 2R_21068757_SNP [dm6]	A	C	1.811e^-5	0.547	SYNONYMOUS_CODING Cht9 EXON CR44703	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	19740320	3R_19740320_SNP [dm3] 3R_23914598_SNP [dm6]	T	A	1.836e^-5	0.547	INTRON sba	TF binding site mE1_TFBS_Kr
3R	21060754	3R_21060754_SNP [dm3] 3R_25235032_SNP [dm6]	A	G	1.855e^-5	0.547	SYNONYMOUS_CODING CG10420	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	3245123	X_3245123_SNP [dm3] X_3351090_SNP [dm6]	C	T	1.879e^-5	0.547	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16726580	X_16726580_SNP [dm3] X_16832547_SNP [dm6]	A	T	1.918e^-5	0.547	INTRON CG13004	TF binding site BDTNP1_TFBS_twi
3R	20057189	3R_20057189_DEL [dm3] 3R_24231467_DEL [dm6]	AAGAA	A	1.978e^-5	0.547	UPSTREAM CR45217 INTRON mask EXON CR44092	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_Trl
3R	25946474	3R_25946474_SNP [dm3] 3R_30120752_SNP [dm6]	C	T	2.110e^-5	0.547	SYNONYMOUS_CODING sima UTR_3_PRIME sima	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	24045932	3R_24045932_SNP [dm3] 3R_28220210_SNP [dm6]	C	T	2.123e^-5	0.547	INTRON CG34354
2R	9924871	2R_9924871_SNP [dm3] 2R_14037366_SNP [dm6]	G	A	2.150e^-5	0.547	INTRON mam	TF binding site mE1_TFBS_HSA
3R	20420739	3R_20420739_SNP [dm3] 3R_24595017_SNP [dm6]	C	T	2.200e^-5	0.547	INTRON mld	TF binding site BDTNP1_TFBS_twi
X	17891056	X_17891056_INS [dm3] X_17997023_INS [dm6]	A	AA	2.200e^-5	0.547	INTRON Sh
3R	24142212	3R_24142212_SNP [dm3] 3R_28316490_SNP [dm6]	T	C	2.229e^-5	0.547	INTERGENIC
3L	13780404	3L_13780404_SNP [dm3] 3L_13787304_SNP [dm6]	A	C	2.248e^-5	0.547	INTRON bru-3
3L	10648482	3L_10648482_SNP [dm3] 3L_10655382_SNP [dm6]	A	T	2.280e^-5	0.547	INTRON CG32066
X	17906872	X_17906872_SNP [dm3] X_18012839_SNP [dm6]	C	A	2.286e^-5	0.547	INTRON Sh
3L	5404049	3L_5404049_SNP [dm3] 3L_5410949_SNP [dm6]	G	A	2.330e^-5	0.547	INTERGENIC
3R	20433924	3R_20433924_DEL [dm3] 3R_24608202_DEL [dm6]	CCGAAATGC	C	2.373e^-5	0.547	INTRON mld
X	17906847	X_17906847_SNP [dm3] X_18012814_SNP [dm6]	T	C	2.387e^-5	0.547	INTRON Sh
X	4376251	X_4376251_SNP [dm3] X_4482218_SNP [dm6]	C	T	2.404e^-5	0.547	SYNONYMOUS_CODING bi INTRON CR32773
3R	20067388	3R_20067388_SNP [dm3] 3R_24241666_SNP [dm6]	C	G	2.500e^-5	0.547	SYNONYMOUS_CODING mask	TF binding site mE1_TFBS_cad
3R	9917527	3R_9917527_SNP [dm3] 3R_14091805_SNP [dm6]	T	C	2.516e^-5	0.547	DOWNSTREAM CCHa1 INTRON Npc2b
3R	14795572	3R_14795572_SNP [dm3] 3R_18969850_SNP [dm6]	C	T	2.518e^-5	0.547	SYNONYMOUS_CODING CG42613 UTR_3_PRIME CG43732
2L	8179867	2L_8179867_SNP [dm3] 2L_8179867_SNP [dm6]	C	T	2.550e^-5	0.547	SPLICE_SITE_REGION Piezo INTRON Piezo	TF binding site mE1_TFBS_cad
3L	13780395	3L_13780395_SNP [dm3] 3L_13787295_SNP [dm6]	C	T	2.619e^-5	0.547	INTRON bru-3
3L	11115216	3L_11115216_SNP [dm3] 3L_11122116_SNP [dm6]	T	A	2.625e^-5	0.547	SYNONYMOUS_CODING Ufd1-like DOWNSTREAM mRpL2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	17906859	X_17906859_SNP [dm3] X_18012826_SNP [dm6]	G	C	2.744e^-5	0.547	INTRON Sh
3R	25397981	3R_25397981_SNP [dm3] 3R_29572259_SNP [dm6]	C	T	2.761e^-5	0.547	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
X	17906858	X_17906858_SNP [dm3] X_18012825_SNP [dm6]	T	C	2.774e^-5	0.547	INTRON Sh
3R	19483410	3R_19483410_SNP [dm3] 3R_23657688_SNP [dm6]	C	T	2.796e^-5	0.547	INTRON CG31145
X	18926882	X_18926882_SNP [dm3] X_19032849_SNP [dm6]	T	C	2.803e^-5	0.547	INTERGENIC
3R	19845243	3R_19845243_SNP [dm3] 3R_24019521_SNP [dm6]	T	A	2.810e^-5	0.547	INTRON KrT95D
2R	6372638	2R_6372638_SNP [dm3] 2R_10485133_SNP [dm6]	T	G	2.815e^-5	0.547	UTR_5_PRIME pre-lola-G INTRON lola & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
3L	17467987	3L_17467987_SNP [dm3] 3L_17474887_SNP [dm6]	C	G	2.817e^-5	0.547	SPLICE_SITE_REGION CG7580 UPSTREAM CG7580 DOWNSTREAM CG7589 INTRON CG7580	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad
3R	20419243	3R_20419243_SNP [dm3] 3R_24593521_SNP [dm6]	A	C	2.833e^-5	0.547	INTRON mld	TF binding site mE1_TFBS_sens
3L	10648477	3L_10648477_SNP [dm3] 3L_10655377_SNP [dm6]	G	A	2.837e^-5	0.547	INTRON CG32066
3R	20059848	3R_20059848_SNP [dm3] 3R_24234126_SNP [dm6]	G	T	2.897e^-5	0.547	UPSTREAM mask INTRON mask	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	7121606	2R_7121606_SNP [dm3] 2R_11234101_SNP [dm6]	C	T	2.923e^-5	0.547	SYNONYMOUS_CODING CG13228 UPSTREAM CG13218
3R	25431860	3R_25431860_SNP [dm3] 3R_29606138_SNP [dm6]	C	A	2.933e^-5	0.547	INTRON alph
3R	21178074	3R_21178074_SNP [dm3] 3R_25352352_SNP [dm6]	G	T	2.982e^-5	0.547	DOWNSTREAM Fur1 INTRON Fur1
3L	3660462	3L_3660462_SNP [dm3] 3L_3660462_SNP [dm6]	C	G	3.001e^-5	0.547	DOWNSTREAM CG43098 INTERGENIC
2L	4690860	2L_4690860_SNP [dm3] 2L_4690860_SNP [dm6]	C	T	3.033e^-5	0.547	UPSTREAM CG3251 INTERGENIC
3L	2055449	3L_2055449_SNP [dm3] 3L_2055449_SNP [dm6]	A	C	3.068e^-5	0.547	SYNONYMOUS_CODING sls INTRON sls	TF binding site mE1_TFBS_sens
2R	15129621	2R_15129621_SNP [dm3] 2R_19242116_SNP [dm6]	T	C	3.073e^-5	0.547	INTRON cora
3R	15905117	3R_15905117_SNP [dm3] 3R_20079395_SNP [dm6]	C	A	3.078e^-5	0.547	INTERGENIC
3R	19904863	3R_19904863_SNP [dm3] 3R_24079141_SNP [dm6]	A	C	3.229e^-5	0.547	INTRON 4EHP
3L	3361917	3L_3361917_SNP [dm3] 3L_3361917_SNP [dm6]	C	T	3.229e^-5	0.547	SYNONYMOUS_CODING kst	TF binding site mE1_TFBS_cad
2R	4120072	2R_4120072_SNP [dm3] 2R_8232567_SNP [dm6]	A	G	3.279e^-5	0.547	UPSTREAM dpn INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	4120102	2R_4120102_SNP [dm3] 2R_8232597_SNP [dm6]	G	T	3.279e^-5	0.547	UPSTREAM dpn INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	3262966	2L_3262966_SNP [dm3] 2L_3262966_SNP [dm6]	G	C	3.317e^-5	0.547	UPSTREAM CR45338 INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

3μg/mL survivorship phenotype phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results