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=5.002e^-3)
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

1219 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	20188889	2R_20188889_SNP [dm3] 2R_24301366_SNP [dm6]	T	G	3.922e^-6	0.876	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	13993156	2R_13993156_SNP [dm3] 2R_18105651_SNP [dm6]	T	G	9.479e^-6	0.876	INTRON CG5756
X	21910607	X_21910607_SNP [dm3] X_22508771_SNP [dm6]	C	A	2.431e^-5	0.876	DOWNSTREAM l_1_G0196 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	970831	3L_970831_SNP [dm3] 3L_970831_SNP [dm6]	A	G	2.492e^-5	0.876	INTRON Glut1
2R	19886410	2R_19886410_SNP [dm3] 2R_23998887_SNP [dm6]	G	A	3.646e^-5	0.876	SYNONYMOUS_CODING Unc-89	TF binding site mE1_TFBS_chinmo
2L	1068382	2L_1068382_SNP [dm3] 2L_1068382_SNP [dm6]	G	A	3.802e^-5	0.876	INTRON S	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	10886371	2R_10886371_SNP [dm3] 2R_14998866_SNP [dm6]	T	C	4.157e^-5	0.876	INTERGENIC
3L	2998162	3L_2998162_SNP [dm3] 3L_2998162_SNP [dm6]	A	T	4.502e^-5	0.876	INTERGENIC
2L	10747823	2L_10747823_SNP [dm3] 2L_10747823_SNP [dm6]	G	A	5.611e^-5	0.876	INTRON CG17124	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10604306	3R_10604306_SNP [dm3] 3R_14778584_SNP [dm6]	T	C	5.754e^-5	0.876	INTRON jvl
3L	2610285	3L_2610285_SNP [dm3] 3L_2610285_SNP [dm6]	C	T	5.767e^-5	0.876	UTR_3_PRIME Pxn INTRON Pxn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	14425262	3R_14425262_SNP [dm3] 3R_18599540_SNP [dm6]	C	T	6.614e^-5	0.876	SYNONYMOUS_CODING CG14305 INTRON qin & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	17693124	3L_17693124_SNP [dm3] 3L_17700024_SNP [dm6]	G	T	6.802e^-5	0.876	INTRON Ccn
X	17167501	X_17167501_SNP [dm3] X_17273468_SNP [dm6]	A	G	7.039e^-5	0.876	INTRON f	TF binding site mE1_TFBS_cad
3R	11618443	3R_11618443_SNP [dm3] 3R_15792721_SNP [dm6]	A	G	7.209e^-5	0.876	UTR_5_PRIME Acyp2 UPSTREAM c_3_G	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Ubx
2L	7207281	2L_7207281_SNP [dm3] 2L_7207281_SNP [dm6]	T	C	7.746e^-5	0.876	SYNONYMOUS_CODING CG13784 UTR_3_PRIME CG13784
2L	13321376	2L_13321376_SNP [dm3] 2L_13321376_SNP [dm6]	A	T	7.850e^-5	0.876	INTRON CG43778
2L	1050940	2L_1050940_SNP [dm3] 2L_1050940_SNP [dm6]	G	T	7.858e^-5	0.876	UTR_3_PRIME S DOWNSTREAM S
2L	1050942	2L_1050942_SNP [dm3] 2L_1050942_SNP [dm6]	A	T	7.858e^-5	0.876	UTR_3_PRIME S DOWNSTREAM S
3L	2659050	3L_2659050_SNP [dm3] 3L_2659050_SNP [dm6]	T	C	7.912e^-5	0.876	SYNONYMOUS_CODING Fife UTR_3_PRIME Fife UPSTREAM CG33233	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_chinmo
2L	19684274	2L_19684274_SNP [dm3] 2L_19684274_SNP [dm6]	T	C	7.950e^-5	0.876	INTRON Lar	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1051015	2L_1051015_SNP [dm3] 2L_1051015_SNP [dm6]	T	A	7.962e^-5	0.876	UTR_3_PRIME S DOWNSTREAM S
3L	2708979	3L_2708979_SNP [dm3] 3L_2708979_SNP [dm6]	T	C	7.975e^-5	0.876	INTRON Fife
3R	9784390	3R_9784390_SNP [dm3] 3R_13958668_SNP [dm6]	T	A	8.007e^-5	0.876	UPSTREAM Ipp INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	9784391	3R_9784391_SNP [dm3] 3R_13958669_SNP [dm6]	T	A	8.007e^-5	0.876	UPSTREAM Ipp INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	13541893	3L_13541893_INS [dm3] 3L_13548793_INS [dm6]	C	CGGACAC	8.019e^-5	0.876	INTRON bru-3
2L	15101700	2L_15101700_SNP [dm3] 2L_15101700_SNP [dm6]	G	C	8.180e^-5	0.876	INTERGENIC
3L	3039454	3L_3039454_SNP [dm3] 3L_3039454_SNP [dm6]	T	C	8.770e^-5	0.876	SYNONYMOUS_CODING CG2162	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2L	11361516	2L_11361516_SNP [dm3] 2L_11361516_SNP [dm6]	T	C	8.952e^-5	0.876	INTRON salr	regulatory region REDfly_CRMs
2R	12456846	2R_12456846_SNP [dm3] 2R_16569341_SNP [dm6]	G	A	8.982e^-5	0.876	SYNONYMOUS_CODING CG4945 DOWNSTREAM RpS15	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	12456810	2R_12456810_SNP [dm3] 2R_16569305_SNP [dm6]	A	G	1.077e^-4	0.876	SYNONYMOUS_CODING CG4945 DOWNSTREAM RpS15	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	2610341	3L_2610341_SNP [dm3] 3L_2610341_SNP [dm6]	G	A	1.085e^-4	0.876	UTR_3_PRIME Pxn INTRON Pxn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	2782693	2L_2782693_SNP [dm3] 2L_2782693_SNP [dm6]	A	G	1.119e^-4	0.876	UTR_3_PRIME Syt1
2L	16317947	2L_16317947_SNP [dm3] 2L_16317947_SNP [dm6]	C	G	1.120e^-4	0.876	INTRON cact	TF binding site BDTNP1_TFBS_twi
2L	10021661	2L_10021661_SNP [dm3] 2L_10021661_SNP [dm6]	C	G	1.129e^-4	0.876	INTERGENIC
2L	10753216	2L_10753216_SNP [dm3] 2L_10753216_SNP [dm6]	A	C	1.153e^-4	0.876	INTRON CG17124
3R	9151822	3R_9151822_SNP [dm3] 3R_13326100_SNP [dm6]	T	C	1.155e^-4	0.876	INTERGENIC
X	19896549	X_19896549_SNP [dm3] X_20002516_SNP [dm6]	G	A	1.220e^-4	0.876	UPSTREAM CG17003 INTERGENIC
X	11139011	X_11139011_SNP [dm3] X_11244978_SNP [dm6]	C	G	1.221e^-4	0.876	INTRON CG44422
2L	15343672	2L_15343672_DEL [dm3] 2L_15343672_DEL [dm6]	AAAT	A	1.230e^-4	0.876	INTERGENIC
2L	15343677	2L_15343677_SNP [dm3] 2L_15343677_SNP [dm6]	A	T	1.230e^-4	0.876	INTERGENIC
2L	15343679	2L_15343679_SNP [dm3] 2L_15343679_SNP [dm6]	T	C	1.230e^-4	0.876	INTERGENIC
2L	15343680	2L_15343680_SNP [dm3] 2L_15343680_SNP [dm6]	T	A	1.230e^-4	0.876	INTERGENIC
2L	15343689	2L_15343689_SNP [dm3] 2L_15343689_SNP [dm6]	T	A	1.230e^-4	0.876	INTERGENIC
2L	4679672	2L_4679672_SNP [dm3] 2L_4679672_SNP [dm6]	G	T	1.249e^-4	0.876	INTERGENIC
2L	2663711	2L_2663711_SNP [dm3] 2L_2663711_SNP [dm6]	T	A	1.283e^-4	0.876	INTERGENIC
3R	10604354	3R_10604354_SNP [dm3] 3R_14778632_SNP [dm6]	T	G	1.290e^-4	0.876	INTRON jvl
X	12130287	X_12130287_SNP [dm3] X_12236254_SNP [dm6]	A	C	1.296e^-4	0.876	UPSTREAM CG32655 INTRON Ten-a
2L	3714053	2L_3714053_SNP [dm3] 2L_3714053_SNP [dm6]	G	C	1.311e^-4	0.876	UPSTREAM CG31955 & 1 other INTRON CG2818	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	21923850	X_21923850_SNP [dm3] X_22522014_SNP [dm6]	A	G	1.320e^-4	0.876	INTRON CG17600	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA transposable element FlyBase
2R	9455395	2R_9455395_SNP [dm3] 2R_13567890_SNP [dm6]	T	A	1.323e^-4	0.876	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Stat92E mE1_TFBS_zfh1
2R	13503985	2R_13503985_SNP [dm3] 2R_17616480_SNP [dm6]	A	G	1.337e^-4	0.876	UPSTREAM snoRNA:Or-aca4 DOWNSTREAM CG44403 INTRON CG10936	TF binding site BDTNP1_TFBS_dl
3L	8197120	3L_8197120_SNP [dm3] 3L_8204020_SNP [dm6]	T	C	1.338e^-4	0.876	DOWNSTREAM CG13679 INTERGENIC
3L	11253610	3L_11253610_SNP [dm3] 3L_11260510_SNP [dm6]	C	T	1.349e^-4	0.876	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_zfh1
2R	18180962	2R_18180962_SNP [dm3] 2R_22293457_SNP [dm6]	T	G	1.352e^-4	0.876	UTR_5_PRIME CG5819 INTRON CG5819
3L	10353951	3L_10353951_SNP [dm3] 3L_10360851_SNP [dm6]	T	A	1.358e^-4	0.876	EXON CR44327	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	3714072	2L_3714072_SNP [dm3] 2L_3714072_SNP [dm6]	A	C	1.386e^-4	0.876	UPSTREAM CG31955 & 1 other INTRON CG2818	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	9867295	3R_9867295_SNP [dm3] 3R_14041573_SNP [dm6]	T	C	1.475e^-4	0.876	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	15289307	3R_15289307_SNP [dm3] 3R_19463585_SNP [dm6]	C	A	1.542e^-4	0.876	UTR_5_PRIME Dys UPSTREAM CG6255 INTRON Dys	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens mE1_TFBS_Trl
3L	14642070	3L_14642070_SNP [dm3] 3L_14648970_SNP [dm6]	C	T	1.555e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642095	3L_14642095_SNP [dm3] 3L_14648995_SNP [dm6]	T	A	1.555e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642098	3L_14642098_SNP [dm3] 3L_14648998_SNP [dm6]	A	T	1.555e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642110	3L_14642110_SNP [dm3] 3L_14649010_SNP [dm6]	T	C	1.555e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	24902209	3R_24902209_SNP [dm3] 3R_29076487_SNP [dm6]	G	A	1.560e^-4	0.876	INTRON CG11873
2L	14032261	2L_14032261_SNP [dm3] 2L_14032261_SNP [dm6]	G	T	1.573e^-4	0.876	UPSTREAM CG18095 EXON CR45284
2L	3453053	2L_3453053_SNP [dm3] 2L_3453053_SNP [dm6]	A	C	1.611e^-4	0.876	SYNONYMOUS_CODING CG12795 DOWNSTREAM Snx1 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	25526883	3R_25526883_SNP [dm3] 3R_29701161_SNP [dm6]	A	T	1.614e^-4	0.876	INTERGENIC	enhancer mE1_CBP_Enhancers
3R	25526886	3R_25526886_SNP [dm3] 3R_29701164_SNP [dm6]	G	T	1.614e^-4	0.876	INTERGENIC	enhancer mE1_CBP_Enhancers
3R	25526896	3R_25526896_SNP [dm3] 3R_29701174_SNP [dm6]	G	T	1.614e^-4	0.876	INTERGENIC	enhancer mE1_CBP_Enhancers
2L	16222318	2L_16222318_SNP [dm3] 2L_16222318_SNP [dm6]	A	G	1.634e^-4	0.876	INTERGENIC
2L	3712625	2L_3712625_SNP [dm3] 2L_3712625_SNP [dm6]	C	A	1.634e^-4	0.876	NON_SYNONYMOUS_CODING CG31955 UPSTREAM cutlet & 1 other INTRON CG31955	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_Ubx
X	2730005	X_2730005_SNP [dm3] X_2835972_SNP [dm6]	T	C	1.646e^-4	0.876	INTRON kirre
X	16082234	X_16082234_SNP [dm3] X_16188201_SNP [dm6]	T	C	1.646e^-4	0.876	INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
3R	18640485	3R_18640485_SNP [dm3] 3R_22814763_SNP [dm6]	C	A	1.648e^-4	0.876	SYNONYMOUS_CODING CG13840
X	7136782	X_7136782_SNP [dm3] X_7242749_SNP [dm6]	C	A	1.659e^-4	0.876	DOWNSTREAM CG9650 INTRON CR44357	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad
3R	10604335	3R_10604335_SNP [dm3] 3R_14778613_SNP [dm6]	G	A	1.666e^-4	0.876	INTRON jvl
X	18213027	X_18213027_SNP [dm3] X_18318994_SNP [dm6]	T	G	1.697e^-4	0.876	INTRON CG6023
3R	24807557	3R_24807557_SNP [dm3] 3R_28981835_SNP [dm6]	C	T	1.721e^-4	0.876	INTERGENIC
3L	17976841	3L_17976841_DEL [dm3] 3L_17983741_DEL [dm6]	CTATCACTC	C	1.732e^-4	0.876	INTRON Eip75B
2L	7944635	2L_7944635_SNP [dm3] 2L_7944635_SNP [dm6]	C	T	1.733e^-4	0.876	INTRON Snoo
2L	4806904	2L_4806904_SNP [dm3] 2L_4806904_SNP [dm6]	A	G	1.766e^-4	0.876	INTERGENIC
3R	24366641	3R_24366641_SNP [dm3] 3R_28540919_SNP [dm6]	G	A	1.771e^-4	0.876	UPSTREAM Ppn INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	3535725	X_3535725_DEL [dm3] X_3641692_DEL [dm6]	AA	T	1.788e^-4	0.876	INTRON AstA-R1
2L	7946125	2L_7946125_SNP [dm3] 2L_7946125_SNP [dm6]	T	A	1.788e^-4	0.876	INTRON Snoo
X	21923868	X_21923868_SNP [dm3] X_22522032_SNP [dm6]	A	T	1.799e^-4	0.876	INTRON CG17600	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA transposable element FlyBase
3L	14642063	3L_14642063_SNP [dm3] 3L_14648963_SNP [dm6]	T	G	1.827e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
X	20530232	X_20530232_SNP [dm3] X_20659205_SNP [dm6]	A	G	1.829e^-4	0.876	INTRON Cyp6v1
3R	9151836	3R_9151836_SNP [dm3] 3R_13326114_SNP [dm6]	A	G	1.853e^-4	0.876	INTERGENIC
3L	2659386	3L_2659386_SNP [dm3] 3L_2659386_SNP [dm6]	T	G	1.858e^-4	0.876	UPSTREAM CG33233 INTRON Fife	TF binding site mE1_TFBS_chinmo
3L	6600205	3L_6600205_SNP [dm3] 3L_6607105_SNP [dm6]	T	G	1.858e^-4	0.876	INTRON CG8368	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	3536288	X_3536288_SNP [dm3] X_3642255_SNP [dm6]	T	G	1.869e^-4	0.876	INTRON AstA-R1
3L	14642039	3L_14642039_SNP [dm3] 3L_14648939_SNP [dm6]	T	G	1.886e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	14642051	3L_14642051_SNP [dm3] 3L_14648951_SNP [dm6]	T	C	1.886e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	15120596	2L_15120596_SNP [dm3] 2L_15120596_SNP [dm6]	G	A	1.912e^-4	0.876	EXON CR43853
2L	9986084	2L_9986084_SNP [dm3] 2L_9986084_SNP [dm6]	G	A	1.916e^-4	0.876	INTRON bib	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3L	14642109	3L_14642109_SNP [dm3] 3L_14649009_SNP [dm6]	A	T	1.924e^-4	0.876	INTRON dlp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
X	20879685	X_20879685_DEL [dm3] X_21008658_DEL [dm6]	TC	T	1.950e^-4	0.876	INTERGENIC
X	14260204	X_14260204_SNP [dm3] X_14366171_SNP [dm6]	A	G	1.969e^-4	0.876	INTRON dpr8
3R	15321702	3R_15321702_SNP [dm3] 3R_19495980_SNP [dm6]	G	T	2.006e^-4	0.876	INTRON Dys	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2R	19304630	2R_19304630_SNP [dm3] 2R_23417107_SNP [dm6]	T	C	2.006e^-4	0.876	UTR_3_PRIME CG30411 INTRON CG9812	TF binding site mE1_TFBS_HSA

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Phenotype distribution and association to known covariates

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GWAS results