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=6.155e^-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

Covariate	p-value	Significance
wolba	0.08217

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1796 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	5208441	X_5208441_SNP [dm3] X_5314408_SNP [dm6]	G	C	4.885e^-7	0.689	NON_SYNONYMOUS_CODING CG4198 DOWNSTREAM CG15930	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	14675777	3R_14675777_SNP [dm3] 3R_18850055_SNP [dm6]	T	A	7.345e^-7	0.689	UPSTREAM CG18208 DOWNSTREAM CR45633 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	20919249	3R_20919249_SNP [dm3] 3R_25093527_SNP [dm6]	G	A	2.254e^-6	0.954	INTERGENIC
3L	6542226	3L_6542226_SNP [dm3] 3L_6549126_SNP [dm6]	A	T	2.830e^-6	0.954	UTR_3_PRIME sfl
X	5208428	X_5208428_SNP [dm3] X_5314395_SNP [dm6]	T	C	3.078e^-6	0.954	SYNONYMOUS_CODING CG4198 DOWNSTREAM CG15930	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10764650	3R_10764650_SNP [dm3] 3R_14938928_SNP [dm6]	A	G	5.471e^-6	0.954	INTERGENIC
3L	4630672	3L_4630672_SNP [dm3] 3L_4630672_SNP [dm6]	C	G	5.527e^-6	0.954	INTRON axo
3R	16520981	3R_16520981_SNP [dm3] 3R_20695259_SNP [dm6]	C	T	5.752e^-6	0.954	INTRON Oamb
3L	16553341	3L_16553341_SNP [dm3] 3L_16560241_SNP [dm6]	G	T	7.549e^-6	0.954	INTERGENIC
3L	6068385	3L_6068385_SNP [dm3] 3L_6075285_SNP [dm6]	G	C	7.638e^-6	0.954	UPSTREAM CG6610 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens
3L	1325184	3L_1325184_SNP [dm3] 3L_1325184_SNP [dm6]	G	A	7.788e^-6	0.954	UTR_5_PRIME Myo61F UPSTREAM CR45166 INTRON Myo61F	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	8133130	2R_8133130_SNP [dm3] 2R_12245625_SNP [dm6]	G	C	8.297e^-6	0.954	UPSTREAM CG43244 INTERGENIC
3L	12431406	3L_12431406_SNP [dm3] 3L_12438306_SNP [dm6]	C	A	8.464e^-6	0.954	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	12260774	2R_12260774_SNP [dm3] 2R_16373269_SNP [dm6]	G	T	1.026e^-5	0.954	INTERGENIC
2R	19585638	2R_19585638_SNP [dm3] 2R_23698115_SNP [dm6]	C	A	1.066e^-5	0.954	UTR_5_PRIME mRpL43 UPSTREAM CG30183 DOWNSTREAM CG4091	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3L	12411612	3L_12411612_SNP [dm3] 3L_12418512_SNP [dm6]	A	T	1.133e^-5	0.954	UPSTREAM ArfGAP1 INTERGENIC	TF binding site mE1_TFBS_cnc
2R	8133171	2R_8133171_SNP [dm3] 2R_12245666_SNP [dm6]	C	T	1.144e^-5	0.954	UPSTREAM CG43244 INTERGENIC
3R	18792563	3R_18792563_SNP [dm3] 3R_22966841_SNP [dm6]	C	T	1.164e^-5	0.954	SYNONYMOUS_CODING Tpl94D	TF binding site mE1_TFBS_cad
2R	10264871	2R_10264871_SNP [dm3] 2R_14377366_SNP [dm6]	G	A	1.174e^-5	0.954	UPSTREAM Dh44-R1 DOWNSTREAM CG30075 INTERGENIC
3R	18797737	3R_18797737_SNP [dm3] 3R_22972015_SNP [dm6]	G	T	1.271e^-5	0.954	INTERGENIC
3R	14676991	3R_14676991_DEL [dm3] 3R_18851269_DEL [dm6]	CG	T	1.333e^-5	0.954	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
X	6880579	X_6880579_SNP [dm3] X_6986546_SNP [dm6]	G	T	1.351e^-5	0.954	UTR_5_PRIME bou UPSTREAM ogre INTRON ogre	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl
3L	12392251	3L_12392251_SNP [dm3] 3L_12399151_SNP [dm6]	A	G	1.382e^-5	0.954	SYNONYMOUS_CODING CG32104 DOWNSTREAM Smyd4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	16731035	3L_16731035_SNP [dm3] 3L_16737935_SNP [dm6]	G	A	1.398e^-5	0.954	SYNONYMOUS_CODING CG9701	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	12411617	3L_12411617_SNP [dm3] 3L_12418517_SNP [dm6]	A	G	1.536e^-5	0.954	UPSTREAM ArfGAP1 INTERGENIC	TF binding site mE1_TFBS_cnc
3R	25328692	3R_25328692_SNP [dm3] 3R_29502970_SNP [dm6]	T	C	1.538e^-5	0.954	SYNONYMOUS_CODING Trc8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
2R	19905970	2R_19905970_SNP [dm3] 2R_24018447_SNP [dm6]	A	G	1.593e^-5	0.954	SYNONYMOUS_CODING CG3121	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	1368309	3L_1368309_SNP [dm3] 3L_1368309_SNP [dm6]	G	A	1.754e^-5	0.954	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	14676984	3R_14676984_SNP [dm3] 3R_18851262_SNP [dm6]	C	T	1.777e^-5	0.954	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
3R	19995838	3R_19995838_SNP [dm3] 3R_24170116_SNP [dm6]	G	T	1.790e^-5	0.954	UPSTREAM CG5510 INTERGENIC
2L	20412981	2L_20412981_SNP [dm3] 2L_20412981_SNP [dm6]	C	G	1.799e^-5	0.954	INTRON CG10947
3L	897184	3L_897184_SNP [dm3] 3L_897184_SNP [dm6]	A	G	2.093e^-5	0.954	NON_SYNONYMOUS_CODING CG34056 UPSTREAM CG34057
2R	19482135	2R_19482135_SNP [dm3] 2R_23594612_SNP [dm6]	G	C	2.225e^-5	0.954	INTRON apt	TF binding site mE1_TFBS_sens
3L	7111439	3L_7111439_SNP [dm3] 3L_7118339_SNP [dm6]	C	T	2.272e^-5	0.954	SYNONYMOUS_CODING form3	TF binding site mE1_TFBS_chinmo
3R	18797809	3R_18797809_SNP [dm3] 3R_22972087_SNP [dm6]	C	T	2.292e^-5	0.954	INTERGENIC
2R	7286655	2R_7286655_SNP [dm3] 2R_11399150_SNP [dm6]	T	C	2.445e^-5	0.954	DOWNSTREAM tRNA:CR30506 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	8586240	2R_8586240_SNP [dm3] 2R_12698735_SNP [dm6]	T	C	2.448e^-5	0.954	INTERGENIC
2R	19905679	2R_19905679_SNP [dm3] 2R_24018156_SNP [dm6]	C	A	2.478e^-5	0.954	SYNONYMOUS_CODING CG3121 UPSTREAM CG4324	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
3R	18797071	3R_18797071_SNP [dm3] 3R_22971349_SNP [dm6]	C	A	2.565e^-5	0.954	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	8133105	2R_8133105_SNP [dm3] 2R_12245600_SNP [dm6]	A	C	2.656e^-5	0.954	UPSTREAM CG43244 INTERGENIC
3R	19870845	3R_19870845_SNP [dm3] 3R_24045123_SNP [dm6]	A	G	2.780e^-5	0.954	SYNONYMOUS_CODING Rox8	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	11192592	2R_11192592_DEL [dm3] 2R_15305087_DEL [dm6]	CT	C	3.250e^-5	0.954	INTRON Trpm
3L	16991961	3L_16991961_SNP [dm3] 3L_16998861_SNP [dm6]	A	G	3.267e^-5	0.954	SYNONYMOUS_CODING CG3764 UPSTREAM mir-2500	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	20064873	2L_20064873_SNP [dm3] 2L_20064873_SNP [dm6]	G	C	3.298e^-5	0.954	SYNONYMOUS_CODING vls DOWNSTREAM lok	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	8944700	3L_8944700_SNP [dm3] 3L_8951600_SNP [dm6]	A	C	3.307e^-5	0.954	INTRON orb2 & 1 other
3R	15673811	3R_15673811_SNP [dm3] 3R_19848089_SNP [dm6]	A	G	3.341e^-5	0.954	INTRON CG4662	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2R	8133273	2R_8133273_DEL [dm3] 2R_12245768_DEL [dm6]	ACT	A	3.350e^-5	0.954	DOWNSTREAM CR44315 INTERGENIC
3L	1136992	3L_1136992_SNP [dm3] 3L_1136992_SNP [dm6]	T	A	3.423e^-5	0.954	INTERGENIC
3L	16731038	3L_16731038_SNP [dm3] 3L_16737938_SNP [dm6]	T	C	3.557e^-5	0.954	SYNONYMOUS_CODING CG9701	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	17683770	3L_17683770_SNP [dm3] 3L_17690670_SNP [dm6]	A	G	3.585e^-5	0.954	INTRON Ccn
2L	7133482	2L_7133482_SNP [dm3] 2L_7133482_SNP [dm6]	A	C	3.607e^-5	0.954	START_GAINED Pvf3 UTR_5_PRIME Pvf3 INTRON Pvf3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20017195	3R_20017195_SNP [dm3] 3R_24191473_SNP [dm6]	T	C	3.771e^-5	0.954	NON_SYNONYMOUS_CODING jnj
3L	10230695	3L_10230695_SNP [dm3] 3L_10237595_SNP [dm6]	G	A	3.857e^-5	0.954	DOWNSTREAM CR44542 INTERGENIC
3L	9751229	3L_9751229_SNP [dm3] 3L_9758129_SNP [dm6]	T	G	4.051e^-5	0.954	INTRON CG42268
2L	7363705	2L_7363705_SNP [dm3] 2L_7363705_SNP [dm6]	G	A	4.207e^-5	0.954	UTR_5_PRIME Wnt10
2L	3373880	2L_3373880_SNP [dm3] 2L_3373880_SNP [dm6]	G	A	4.403e^-5	0.954	SYNONYMOUS_CODING CG15412 UPSTREAM CG34394	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	12079989	X_12079989_SNP [dm3] X_12185956_SNP [dm6]	C	G	4.460e^-5	0.954	INTRON Ten-a
2L	20474163	2L_20474163_SNP [dm3] 2L_20474163_SNP [dm6]	C	T	4.575e^-5	0.954	UPSTREAM CG43233 INTRON CR44980
3L	13725500	3L_13725500_DEL [dm3] 3L_13732400_DEL [dm6]	ACTGACAGA	A	4.646e^-5	0.954	INTRON bru-3
3L	897188	3L_897188_SNP [dm3] 3L_897188_SNP [dm6]	T	C	4.757e^-5	0.954	SYNONYMOUS_CODING CG34056 UPSTREAM CG34057
3L	6532070	3L_6532070_SNP [dm3] 3L_6538970_SNP [dm6]	T	C	4.758e^-5	0.954	INTRON sfl
3R	15670105	3R_15670105_SNP [dm3] 3R_19844383_SNP [dm6]	C	A	4.871e^-5	0.954	INTERGENIC
X	16606189	X_16606189_SNP [dm3] X_16712156_SNP [dm6]	T	C	4.949e^-5	0.954	NON_SYNONYMOUS_CODING CG13008	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	3546984	X_3546984_INS [dm3] X_3652951_INS [dm6]	T	TC	4.987e^-5	0.954	INTRON AstA-R1
3R	10420289	3R_10420289_SNP [dm3] 3R_14594567_SNP [dm6]	A	T	5.004e^-5	0.954	INTRON stumps	regulatory region REDfly_CRMs
X	5447460	X_5447460_SNP [dm3] X_5553427_SNP [dm6]	T	G	5.036e^-5	0.954	INTRON Vsx2	TF binding site BDTNP1_TFBS_dl
2L	7133460	2L_7133460_SNP [dm3] 2L_7133460_SNP [dm6]	C	T	5.092e^-5	0.954	UTR_5_PRIME Pvf3 INTRON Pvf3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	7199551	3L_7199551_SNP [dm3] 3L_7206451_SNP [dm6]	C	T	5.213e^-5	0.954	INTERGENIC
3L	1136985	3L_1136985_MNP [dm3] 3L_1136985_MNP [dm6]	TTT	CAC	5.336e^-5	0.954	INTERGENIC
2L	20474175	2L_20474175_SNP [dm3] 2L_20474175_SNP [dm6]	C	T	5.487e^-5	0.954	UPSTREAM CG43233 INTRON CR44980
2R	10265199	2R_10265199_SNP [dm3] 2R_14377694_SNP [dm6]	A	C	5.522e^-5	0.954	UPSTREAM Dh44-R1 INTERGENIC
3R	18390972	3R_18390972_SNP [dm3] 3R_22565250_SNP [dm6]	G	A	5.638e^-5	0.954	INTERGENIC
3L	16204363	3L_16204363_SNP [dm3] 3L_16211263_SNP [dm6]	G	T	5.728e^-5	0.954	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	7043067	2R_7043067_SNP [dm3] 2R_11155562_SNP [dm6]	A	G	5.783e^-5	0.954	DOWNSTREAM CG13230 INTRON CG13229
3R	26940100	3R_26940100_SNP [dm3] 3R_31114378_SNP [dm6]	T	C	5.862e^-5	0.954	INTERGENIC	TF binding site mE1_TFBS_inv
3L	3423124	3L_3423124_SNP [dm3] 3L_3423124_SNP [dm6]	A	T	5.872e^-5	0.954	INTRON sty	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	16944520	2L_16944520_SNP [dm3] 2L_16944520_SNP [dm6]	G	A	5.948e^-5	0.954	DOWNSTREAM CR43053 INTERGENIC
3R	16528999	3R_16528999_SNP [dm3] 3R_20703277_SNP [dm6]	T	C	6.024e^-5	0.954	INTRON Oamb
3R	17116277	3R_17116277_SNP [dm3] 3R_21290555_SNP [dm6]	T	C	6.101e^-5	0.954	INTRON SIFaR
3L	7851272	3L_7851272_SNP [dm3] 3L_7858172_SNP [dm6]	A	C	6.318e^-5	0.954	INTRON Pdp1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	18719096	X_18719096_SNP [dm3] X_18825063_SNP [dm6]	G	A	6.327e^-5	0.954	SYNONYMOUS_CODING CG42450	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1263078	3L_1263078_SNP [dm3] 3L_1263078_SNP [dm6]	G	C	6.692e^-5	0.954	INTRON CG9134
3L	16302829	3L_16302829_SNP [dm3] 3L_16309729_SNP [dm6]	A	G	6.844e^-5	0.954	INTRON CR32160
2R	8345647	2R_8345647_SNP [dm3] 2R_12458142_SNP [dm6]	G	T	6.911e^-5	0.954	INTRON Lac	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	1376855	3L_1376855_SNP [dm3] 3L_1376855_SNP [dm6]	T	C	6.924e^-5	0.954	INTRON Ptp61F & 1 other
3R	10904075	3R_10904075_SNP [dm3] 3R_15078353_SNP [dm6]	G	A	7.008e^-5	0.954	DOWNSTREAM CG6974 & 1 other INTERGENIC
2L	7490336	2L_7490336_SNP [dm3] 2L_7490336_SNP [dm6]	C	T	7.048e^-5	0.954	INTRON Ziz
3R	16528700	3R_16528700_SNP [dm3] 3R_20702978_SNP [dm6]	T	A	7.089e^-5	0.954	INTRON Oamb
3L	18645429	3L_18645429_SNP [dm3] 3L_18652329_SNP [dm6]	A	C	7.144e^-5	0.954	INTRON MYPT-75D
2L	21061321	2L_21061321_SNP [dm3] 2L_21061321_SNP [dm6]	T	G	7.231e^-5	0.954	INTRON CG9265
X	20554931	X_20554931_DEL [dm3] X_20683904_DEL [dm6]	CTTAGA	T	7.240e^-5	0.954	INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site mE1_TFBS_GATAe mE1_TFBS_HSA
2R	14165837	2R_14165837_DEL [dm3] 2R_18278332_DEL [dm6]	CGCCC	C	7.316e^-5	0.954	UTR_3_PRIME pen-2 & 1 other DOWNSTREAM sbb & 1 other
3R	22294793	3R_22294793_SNP [dm3] 3R_26469071_SNP [dm6]	A	G	7.401e^-5	0.954	INTRON CG5455
3R	20017063	3R_20017063_SNP [dm3] 3R_24191341_SNP [dm6]	A	G	7.455e^-5	0.954	INTRON jnj
2R	19787719	2R_19787719_SNP [dm3] 2R_23900196_SNP [dm6]	T	C	7.458e^-5	0.954	SYNONYMOUS_CODING Lpt	TF binding site mE1_TFBS_chinmo
3R	13558077	3R_13558077_SNP [dm3] 3R_17732355_SNP [dm6]	T	C	7.466e^-5	0.954	INTRON Lgr1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	10230591	3L_10230591_SNP [dm3] 3L_10237491_SNP [dm6]	G	A	7.475e^-5	0.954	DOWNSTREAM CR44542 INTERGENIC
3L	7852125	3L_7852125_SNP [dm3] 3L_7859025_SNP [dm6]	T	C	7.601e^-5	0.954	INTRON Pdp1
X	11560584	X_11560584_SNP [dm3] X_11666551_SNP [dm6]	T	A	7.800e^-5	0.954	INTRON Ptp10D
3L	6291711	3L_6291711_SNP [dm3] 3L_6298611_SNP [dm6]	T	C	7.874e^-5	0.954	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo

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Phenotype distribution and association to known covariates

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GWAS results