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=1.285e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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	5.6529	0.0592

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1645 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
X	5242623	X_5242623_SNP [dm3] X_5348590_SNP [dm6]	G	C	1.353e^-6	1	INTRON SK
2L	12449841	2L_12449841_SNP [dm3] 2L_12449841_SNP [dm6]	C	A	3.795e^-6	1	SYNONYMOUS_CODING Oatp33Eb	TF binding site mE1_TFBS_cad
3L	15342098	3L_15342098_SNP [dm3] 3L_15348998_SNP [dm6]	A	T	5.357e^-6	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	11943317	2L_11943317_SNP [dm3] 2L_11943317_SNP [dm6]	G	T	5.699e^-6	1	UPSTREAM Cry INTERGENIC	regulatory region REDfly_CRMs
3R	8559004	3R_8559004_SNP [dm3] 3R_12733282_SNP [dm6]	A	G	5.862e^-6	1	INTERGENIC
2L	3496369	2L_3496369_SNP [dm3] 2L_3496369_SNP [dm6]	A	C	6.556e^-6	1	INTRON tim
X	13128834	X_13128834_SNP [dm3] X_13234801_SNP [dm6]	C	T	1.129e^-5	1	INTRON mew	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
3R	8559023	3R_8559023_SNP [dm3] 3R_12733301_SNP [dm6]	G	A	1.220e^-5	1	INTERGENIC
2R	9255505	2R_9255505_SNP [dm3] 2R_13368000_SNP [dm6]	G	T	1.226e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	9255380	2R_9255380_INS [dm3] 2R_13367875_INS [dm6]	T	TA	1.302e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255383	2R_9255383_SNP [dm3] 2R_13367878_SNP [dm6]	G	C	1.302e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	16281741	2R_16281741_SNP [dm3] 2R_20394236_SNP [dm6]	C	A	1.320e^-5	1	INTERGENIC
2R	9255394	2R_9255394_SNP [dm3] 2R_13367889_SNP [dm6]	A	G	1.322e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255415	2R_9255415_SNP [dm3] 2R_13367910_SNP [dm6]	T	A	1.322e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255433	2R_9255433_DEL [dm3] 2R_13367928_DEL [dm6]	TACTTCATTC	T	1.322e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255457	2R_9255457_SNP [dm3] 2R_13367952_SNP [dm6]	A	T	1.322e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255475	2R_9255475_SNP [dm3] 2R_13367970_SNP [dm6]	A	G	1.322e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255386	2R_9255386_SNP [dm3] 2R_13367881_SNP [dm6]	C	A	1.328e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	5826525	2L_5826525_SNP [dm3] 2L_5826525_SNP [dm6]	T	C	1.429e^-5	1	INTRON TrissinR
X	13128674	X_13128674_SNP [dm3] X_13234641_SNP [dm6]	A	G	1.535e^-5	1	INTRON mew	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	9255468	2R_9255468_SNP [dm3] 2R_13367963_SNP [dm6]	T	A	1.571e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	16272332	2R_16272332_SNP [dm3] 2R_20384827_SNP [dm6]	A	G	1.597e^-5	1	INTERGENIC
X	15988441	X_15988441_SNP [dm3] X_16094408_SNP [dm6]	G	T	1.670e^-5	1	NON_SYNONYMOUS_CODING CG42354 UTR_3_PRIME CG42353	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
X	15988456	X_15988456_SNP [dm3] X_16094423_SNP [dm6]	A	G	1.670e^-5	1	NON_SYNONYMOUS_CODING CG42354 UTR_3_PRIME CG42353	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2L	11943324	2L_11943324_SNP [dm3] 2L_11943324_SNP [dm6]	G	A	1.722e^-5	1	UPSTREAM Cry INTERGENIC	regulatory region REDfly_CRMs
2R	9255389	2R_9255389_SNP [dm3] 2R_13367884_SNP [dm6]	T	C	1.801e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	20487344	3L_20487344_SNP [dm3] 3L_20494244_SNP [dm6]	T	A	1.836e^-5	1	UPSTREAM ZnT77C INTRON ZnT77C & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	16272200	2R_16272200_SNP [dm3] 2R_20384695_SNP [dm6]	A	G	1.907e^-5	1	INTERGENIC
2R	9255450	2R_9255450_SNP [dm3] 2R_13367945_SNP [dm6]	C	A	1.963e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	24213347	3R_24213347_SNP [dm3] 3R_28387625_SNP [dm6]	T	C	2.049e^-5	1	INTERGENIC
2L	7542260	2L_7542260_SNP [dm3] 2L_7542260_SNP [dm6]	T	A	2.108e^-5	1	INTRON RapGAP1
2R	9255454	2R_9255454_SNP [dm3] 2R_13367949_SNP [dm6]	G	C	2.124e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	11943305	2L_11943305_SNP [dm3] 2L_11943305_SNP [dm6]	C	A	2.139e^-5	1	UPSTREAM Cry INTERGENIC	regulatory region REDfly_CRMs
3R	21820494	3R_21820494_SNP [dm3] 3R_25994772_SNP [dm6]	A	G	2.287e^-5	1	SYNONYMOUS_CODING Nf1 UTR_3_PRIME Nf1 DOWNSTREAM Nf1
2R	9255462	2R_9255462_SNP [dm3] 2R_13367957_SNP [dm6]	G	T	2.298e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	20487341	3L_20487341_SNP [dm3] 3L_20494241_SNP [dm6]	T	C	2.303e^-5	1	UPSTREAM ZnT77C INTRON ZnT77C & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	16272330	2R_16272330_SNP [dm3] 2R_20384825_SNP [dm6]	A	C	2.376e^-5	1	INTERGENIC
2R	9255387	2R_9255387_INS [dm3] 2R_13367882_INS [dm6]	T	TT	2.405e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255507	2R_9255507_SNP [dm3] 2R_13368002_SNP [dm6]	A	G	2.508e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	20487332	3L_20487332_SNP [dm3] 3L_20494232_SNP [dm6]	C	T	2.611e^-5	1	UPSTREAM ZnT77C INTRON ZnT77C & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	20487349	3L_20487349_DEL [dm3] 3L_20494249_DEL [dm6]	ACAATAATATA...	A	2.682e^-5	1	UPSTREAM ZnT77C INTRON ZnT77C & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	3855385	3L_3855385_SNP [dm3] 3L_3855385_SNP [dm6]	G	A	2.767e^-5	1	INTRON Awh	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
3L	3855412	3L_3855412_SNP [dm3] 3L_3855412_SNP [dm6]	T	C	2.767e^-5	1	INTRON Awh	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
X	6364887	X_6364887_SNP [dm3] X_6470854_SNP [dm6]	C	G	2.801e^-5	1	DOWNSTREAM CG33667 INTRON CG42340
3L	18197987	3L_18197987_SNP [dm3] 3L_18204887_SNP [dm6]	A	G	2.818e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	7087749	3L_7087749_SNP [dm3] 3L_7094649_SNP [dm6]	T	A	2.944e^-5	1	UPSTREAM form3 DOWNSTREAM Cpr65Ec INTERGENIC
3L	672611	3L_672611_SNP [dm3] 3L_672611_SNP [dm6]	T	C	2.991e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad
3R	21820523	3R_21820523_SNP [dm3] 3R_25994801_SNP [dm6]	T	A	3.155e^-5	1	UTR_3_PRIME Nf1 DOWNSTREAM Nf1
2L	19129079	2L_19129079_SNP [dm3] 2L_19129079_SNP [dm6]	C	T	3.227e^-5	1	UTR_3_PRIME l_2_37Cd DOWNSTREAM Aats-asn	TF binding site mE1_TFBS_cad
2L	11943300	2L_11943300_SNP [dm3] 2L_11943300_SNP [dm6]	T	G	3.465e^-5	1	UPSTREAM Cry INTERGENIC	regulatory region REDfly_CRMs
X	2341230	X_2341230_SNP [dm3] X_2447197_SNP [dm6]	A	G	3.470e^-5	1	SYNONYMOUS_CODING boi UPSTREAM z	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
3L	18260151	3L_18260151_SNP [dm3] 3L_18267051_SNP [dm6]	T	A	3.701e^-5	1	INTERGENIC
X	10871717	X_10871717_SNP [dm3] X_10977684_SNP [dm6]	C	A	3.712e^-5	1	INTRON CG42339
3R	12734633	3R_12734633_SNP [dm3] 3R_16908911_SNP [dm6]	G	A	3.754e^-5	1	INTRON iab-8	TF binding site BDTNP1_TFBS_dl
3R	13187998	3R_13187998_SNP [dm3] 3R_17362276_SNP [dm6]	A	C	3.834e^-5	1	INTRON beat-IIa
3L	7087671	3L_7087671_SNP [dm3] 3L_7094571_SNP [dm6]	G	C	3.874e^-5	1	UPSTREAM form3 DOWNSTREAM Cpr65Ec INTERGENIC
3R	14927302	3R_14927302_DEL [dm3] 3R_19101580_DEL [dm6]	TGGAAATTAACTGAT...	T	4.089e^-5	1	INTRON CG6040
2R	19016870	2R_19016870_SNP [dm3] 2R_23129347_SNP [dm6]	C	T	4.134e^-5	1	DOWNSTREAM CR44456 INTRON CG3215
2R	16301708	2R_16301708_SNP [dm3] 2R_20414203_SNP [dm6]	G	T	4.315e^-5	1	INTERGENIC
2R	9255392	2R_9255392_SNP [dm3] 2R_13367887_SNP [dm6]	A	C	4.374e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	6732880	X_6732880_SNP [dm3] X_6838847_SNP [dm6]	A	G	4.416e^-5	1	UTR_3_PRIME CG14435 DOWNSTREAM nonC & 1 other
3L	15282736	3L_15282736_SNP [dm3] 3L_15289636_SNP [dm6]	A	G	4.427e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	17229717	3R_17229717_INS [dm3] 3R_21403995_INS [dm6]	A	ATAAACGGAAAAGTGCTACT...	4.482e^-5	1	INTRON CG7907
2R	9255416	2R_9255416_SNP [dm3] 2R_13367911_SNP [dm6]	A	C	4.535e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7087720	3L_7087720_SNP [dm3] 3L_7094620_SNP [dm6]	G	T	4.546e^-5	1	UPSTREAM form3 DOWNSTREAM Cpr65Ec INTERGENIC
2L	2853928	2L_2853928_SNP [dm3] 2L_2853928_SNP [dm6]	T	A	4.573e^-5	1	INTRON CG3104	TF binding site mE1_TFBS_cnc
3R	10872737	3R_10872737_SNP [dm3] 3R_15047015_SNP [dm6]	C	T	4.671e^-5	1	INTERGENIC
2R	9255166	2R_9255166_SNP [dm3] 2R_13367661_SNP [dm6]	C	T	4.675e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	20487334	3L_20487334_SNP [dm3] 3L_20494234_SNP [dm6]	A	G	4.762e^-5	1	UPSTREAM ZnT77C INTRON ZnT77C & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	9251708	2R_9251708_SNP [dm3] 2R_13364203_SNP [dm6]	C	T	4.790e^-5	1	INTERGENIC
3L	20487336	3L_20487336_DEL [dm3] 3L_20494236_DEL [dm6]	GT	G	4.898e^-5	1	UPSTREAM ZnT77C INTRON ZnT77C & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	3469337	2L_3469337_SNP [dm3] 2L_3469337_SNP [dm6]	G	T	4.967e^-5	1	SYNONYMOUS_CODING CG3238 UPSTREAM CG31776	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	13189019	3R_13189019_SNP [dm3] 3R_17363297_SNP [dm6]	C	A	5.019e^-5	1	INTRON beat-IIa
3L	13855357	3L_13855357_SNP [dm3] 3L_13862257_SNP [dm6]	T	C	5.237e^-5	1	INTRON CG8745
2L	3555787	2L_3555787_SNP [dm3] 2L_3555787_SNP [dm6]	G	C	5.456e^-5	1	INTERGENIC
X	2280040	X_2280040_DEL [dm3] X_2386007_DEL [dm6]	TT	A	5.501e^-5	1	INTRON PsGEF	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8812098	3L_8812098_SNP [dm3] 3L_8818998_SNP [dm6]	T	G	5.584e^-5	1	INTERGENIC
2L	11943323	2L_11943323_INS [dm3] 2L_11943323_INS [dm6]	A	GTTTTGGTCGGTTGTAG...	5.665e^-5	1	UPSTREAM Cry INTERGENIC	regulatory region REDfly_CRMs
3L	7889737	3L_7889737_SNP [dm3] 3L_7896637_SNP [dm6]	G	T	5.682e^-5	1	UTR_3_PRIME pbl DOWNSTREAM eIF4E-5
2R	8938911	2R_8938911_SNP [dm3] 2R_13051406_SNP [dm6]	T	A	5.786e^-5	1	INTERGENIC
2R	9255486	2R_9255486_SNP [dm3] 2R_13367981_SNP [dm6]	T	A	5.870e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	14975405	3R_14975405_SNP [dm3] 3R_19149683_SNP [dm6]	T	G	5.900e^-5	1	DOWNSTREAM CR44107 INTRON CG5835
3L	3855438	3L_3855438_SNP [dm3] 3L_3855438_SNP [dm6]	T	C	5.912e^-5	1	INTRON Awh	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
3R	12178368	3R_12178368_SNP [dm3] 3R_16352646_SNP [dm6]	C	T	6.037e^-5	1	INTRON CG10311
X	8476544	X_8476544_SNP [dm3] X_8582511_SNP [dm6]	T	G	6.088e^-5	1	INTRON CG12065
2L	16797926	2L_16797926_DEL [dm3] 2L_16797926_DEL [dm6]	GAGC	G	6.100e^-5	1
3L	20490635	3L_20490635_SNP [dm3] 3L_20497535_SNP [dm6]	T	A	6.205e^-5	1	UTR_5_PRIME CG32425 DOWNSTREAM CG6020 INTRON CG32425	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	6209418	X_6209418_SNP [dm3] X_6315385_SNP [dm6]	C	T	6.208e^-5	1	INTRON CG15894
X	6613810	X_6613810_SNP [dm3] X_6719777_SNP [dm6]	C	A	6.212e^-5	1	DOWNSTREAM CG3168 & 1 other INTERGENIC
3L	20487324	3L_20487324_DEL [dm3] 3L_20494224_DEL [dm6]	ACAAAAA	A	6.225e^-5	1	UPSTREAM ZnT77C INTRON ZnT77C & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	2279797	X_2279797_SNP [dm3] X_2385764_SNP [dm6]	G	T	6.262e^-5	1	INTRON PsGEF	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	15282742	3L_15282742_SNP [dm3] 3L_15289642_SNP [dm6]	C	T	6.320e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	20830451	2L_20830451_SNP [dm3] 2L_20830451_SNP [dm6]	G	T	6.342e^-5	1	NON_SYNONYMOUS_CODING CG31673 UPSTREAM CG31674
3L	18150913	3L_18150913_SNP [dm3] 3L_18157813_SNP [dm6]	A	T	6.396e^-5	1	INTRON CG13699
2R	17431811	2R_17431811_SNP [dm3] 2R_21544306_SNP [dm6]	C	T	6.442e^-5	1	INTRON Egfr	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_h mE1_TFBS_HSA
2R	14321827	2R_14321827_DEL [dm3] 2R_18434322_DEL [dm6]	ACAAA	A	6.467e^-5	1	INTRON CG30118
2R	9255398	2R_9255398_SNP [dm3] 2R_13367893_SNP [dm6]	C	T	6.470e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255399	2R_9255399_DEL [dm3] 2R_13367894_DEL [dm6]	TA	T	6.470e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9255407	2R_9255407_SNP [dm3] 2R_13367902_SNP [dm6]	T	A	6.470e^-5	1	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7115610	3L_7115610_SNP [dm3] 3L_7122510_SNP [dm6]	T	C	6.527e^-5	1	SYNONYMOUS_CODING form3 DOWNSTREAM msl-3	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

N phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results