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=6.931e^-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
In_3R_K	0.08866

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	6.606	0.0368

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2106 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
3R	14470081	3R_14470081_SNP [dm3] 3R_18644359_SNP [dm6]	G	C	8.062e^-7	0.878	INTRON qin
X	5445429	X_5445429_SNP [dm3] X_5551396_SNP [dm6]	C	T	1.170e^-6	0.878	INTRON Vsx2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
X	6205618	X_6205618_SNP [dm3] X_6311585_SNP [dm6]	T	G	1.522e^-6	0.878	INTRON CG15894
3L	826239	3L_826239_SNP [dm3] 3L_826239_SNP [dm6]	A	T	2.618e^-6	0.878	DOWNSTREAM CG13900 & 2 others INTERGENIC
2R	8611939	2R_8611939_SNP [dm3] 2R_12724434_SNP [dm6]	A	G	3.096e^-6	0.878	INTRON CG42663
2R	13833195	2R_13833195_SNP [dm3] 2R_17945690_SNP [dm6]	A	G	3.675e^-6	0.878	INTERGENIC
3R	14470817	3R_14470817_SNP [dm3] 3R_18645095_SNP [dm6]	C	A	6.164e^-6	0.878	SYNONYMOUS_CODING qin
3R	14470809	3R_14470809_SNP [dm3] 3R_18645087_SNP [dm6]	A	G	6.240e^-6	0.878	NON_SYNONYMOUS_CODING qin
3R	21408483	3R_21408483_SNP [dm3] 3R_25582761_SNP [dm6]	C	T	6.667e^-6	0.878	SYNONYMOUS_CODING CG4582 INTRON msi	TF binding site mE1_TFBS_cad
3L	20338347	3L_20338347_SNP [dm3] 3L_20345247_SNP [dm6]	T	C	6.832e^-6	0.878	DOWNSTREAM Spn77Bc & 1 other EXON CR45385
3L	19255763	3L_19255763_SNP [dm3] 3L_19262663_SNP [dm6]	T	C	7.607e^-6	0.878	UTR_3_PRIME Max DOWNSTREAM Max & 1 other	TF binding site mE1_TFBS_cad
2R	14559079	2R_14559079_SNP [dm3] 2R_18671574_SNP [dm6]	A	G	1.145e^-5	0.878	INTRON edl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15064256	2R_15064256_SNP [dm3] 2R_19176751_SNP [dm6]	T	C	1.168e^-5	0.878	SPLICE_SITE_REGION CG10737 INTRON CG10737
2L	4901956	2L_4901956_SNP [dm3] 2L_4901956_SNP [dm6]	A	G	1.224e^-5	0.878	INTRON CG3036	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	6205634	X_6205634_SNP [dm3] X_6311601_SNP [dm6]	A	C	1.262e^-5	0.878	INTRON CG15894
X	6205670	X_6205670_DEL [dm3] X_6311637_DEL [dm6]	CTTTC	C	1.262e^-5	0.878	INTRON CG15894
X	5445409	X_5445409_SNP [dm3] X_5551376_SNP [dm6]	C	T	1.287e^-5	0.878	INTRON Vsx2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
X	5507374	X_5507374_SNP [dm3] X_5613341_SNP [dm6]	A	G	1.343e^-5	0.878	UTR_3_PRIME CG34435 DOWNSTREAM Vsx1	TF binding site mE1_TFBS_bab1
2L	1197440	2L_1197440_SNP [dm3] 2L_1197440_SNP [dm6]	C	T	1.345e^-5	0.878	DOWNSTREAM CG5001 INTERGENIC
3R	8138129	3R_8138129_SNP [dm3] 3R_12312407_SNP [dm6]	G	A	1.360e^-5	0.878	NON_SYNONYMOUS_CODING CG4066	TF binding site mE1_TFBS_sens
3R	18541902	3R_18541902_SNP [dm3] 3R_22716180_SNP [dm6]	A	G	1.555e^-5	0.878	SYNONYMOUS_CODING wge	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	1099224	2R_1099224_SNP [dm3] 2R_5211719_SNP [dm6]	A	T	1.601e^-5	0.878	INTRON Nipped-A	transposable element FlyBase
X	6417998	X_6417998_SNP [dm3] X_6523965_SNP [dm6]	A	T	1.743e^-5	0.878	UTR_5_PRIME CG42340 UPSTREAM CG3918	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	21864326	3R_21864326_SNP [dm3] 3R_26038604_SNP [dm6]	C	T	1.794e^-5	0.878	DOWNSTREAM E_spl_m7-HLH INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
2L	3104072	2L_3104072_SNP [dm3] 2L_3104072_SNP [dm6]	A	C	1.878e^-5	0.878	INTRON toc
3L	9174610	3L_9174610_SNP [dm3] 3L_9181510_SNP [dm6]	G	A	1.912e^-5	0.878	INTRON Rdl
3R	26095970	3R_26095970_SNP [dm3] 3R_30270248_SNP [dm6]	C	A	2.100e^-5	0.878	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	23254918	3R_23254918_SNP [dm3] 3R_27429196_SNP [dm6]	A	G	2.196e^-5	0.878	INTRON side
3R	22381901	3R_22381901_SNP [dm3] 3R_26556179_SNP [dm6]	A	T	2.292e^-5	0.878	INTRON scrib	TF binding site mE1_TFBS_cnc
2L	8221681	2L_8221681_SNP [dm3] 2L_8221681_SNP [dm6]	G	C	2.294e^-5	0.878	SYNONYMOUS_CODING Pvr UPSTREAM Snx6
3R	13797907	3R_13797907_SNP [dm3] 3R_17972185_SNP [dm6]	A	G	2.301e^-5	0.878	INTRON cpo
2R	15064258	2R_15064258_SNP [dm3] 2R_19176753_SNP [dm6]	C	T	2.303e^-5	0.878	INTRON CG10737
3L	4724709	3L_4724709_SNP [dm3] 3L_4724709_SNP [dm6]	T	C	2.321e^-5	0.878	INTRON RhoGEF64C
3L	10732808	3L_10732808_SNP [dm3] 3L_10739708_SNP [dm6]	T	A	2.355e^-5	0.878	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	788550	3L_788550_SNP [dm3] 3L_788550_SNP [dm6]	A	T	2.558e^-5	0.878	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
X	11938442	X_11938442_SNP [dm3] X_12044409_SNP [dm6]	T	C	2.746e^-5	0.878	INTRON CR43960 & 1 other
X	4274263	X_4274263_SNP [dm3] X_4380230_SNP [dm6]	C	A	2.781e^-5	0.878	UPSTREAM CG12688 INTERGENIC
2R	6788862	2R_6788862_SNP [dm3] 2R_10901357_SNP [dm6]	G	T	2.815e^-5	0.878	INTERGENIC
X	3068864	X_3068864_SNP [dm3] X_3174831_SNP [dm6]	G	T	2.823e^-5	0.878	UPSTREAM CG3939 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3R	13589843	3R_13589843_SNP [dm3] 3R_17764121_SNP [dm6]	A	G	2.830e^-5	0.878	UPSTREAM TyrR INTERGENIC
2R	1099034	2R_1099034_SNP [dm3] 2R_5211529_SNP [dm6]	A	T	2.837e^-5	0.878	INTRON Nipped-A
3R	11160926	3R_11160926_SNP [dm3] 3R_15335204_SNP [dm6]	C	T	3.030e^-5	0.878	SYNONYMOUS_CODING Sra-1	TF binding site mE1_TFBS_chinmo
3L	2124997	3L_2124997_DEL [dm3] 3L_2124997_DEL [dm6]	AA	A	3.078e^-5	0.878	INTRON zormin
2R	4637431	2R_4637431_SNP [dm3] 2R_8749926_SNP [dm6]	C	T	3.113e^-5	0.878	INTRON CG8740
X	3068870	X_3068870_SNP [dm3] X_3174837_SNP [dm6]	C	T	3.143e^-5	0.878	UPSTREAM CG3939 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3R	23254891	3R_23254891_SNP [dm3] 3R_27429169_SNP [dm6]	T	A	3.149e^-5	0.878	INTRON side
3L	21771994	3L_21771994_SNP [dm3] 3L_21778894_SNP [dm6]	C	G	3.150e^-5	0.878	DOWNSTREAM CG42552 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	10082453	X_10082453_SNP [dm3] X_10188420_SNP [dm6]	T	G	3.190e^-5	0.878	NON_SYNONYMOUS_CODING CG43902 INTRON CR44894
X	3068883	X_3068883_SNP [dm3] X_3174850_SNP [dm6]	T	C	3.200e^-5	0.878	UPSTREAM CG3939 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3R	19457836	3R_19457836_SNP [dm3] 3R_23632114_SNP [dm6]	A	G	3.202e^-5	0.878	NON_SYNONYMOUS_CODING CG31145 INTRON CG31145	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	3630357	2L_3630357_SNP [dm3] 2L_3630357_SNP [dm6]	T	A	3.340e^-5	0.878	INTRON for
3R	23250529	3R_23250529_SNP [dm3] 3R_27424807_SNP [dm6]	A	C	3.350e^-5	0.878	INTRON side
3L	1369234	3L_1369234_SNP [dm3] 3L_1369234_SNP [dm6]	C	A	3.377e^-5	0.878	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
3R	25236437	3R_25236437_SNP [dm3] 3R_29410715_SNP [dm6]	C	A	3.442e^-5	0.878	INTRON Ptp99A
X	3068874	X_3068874_SNP [dm3] X_3174841_SNP [dm6]	G	C	3.494e^-5	0.878	UPSTREAM CG3939 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
2L	3104089	2L_3104089_SNP [dm3] 2L_3104089_SNP [dm6]	G	A	3.498e^-5	0.878	INTRON toc
2R	12967499	2R_12967499_SNP [dm3] 2R_17079994_SNP [dm6]	T	G	3.503e^-5	0.878	INTRON CG30460
3R	26095935	3R_26095935_INS [dm3] 3R_30270213_INS [dm6]	T	TATT	3.568e^-5	0.878	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	16301894	X_16301894_SNP [dm3] X_16407861_SNP [dm6]	G	A	3.603e^-5	0.878	UPSTREAM CG4301 INTRON CG4301
3L	17978870	3L_17978870_SNP [dm3] 3L_17985770_SNP [dm6]	G	A	3.628e^-5	0.878	INTRON Eip75B	TF binding site BDTNP1_TFBS_dl
2L	6820918	2L_6820918_SNP [dm3] 2L_6820918_SNP [dm6]	G	A	3.643e^-5	0.878	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	6622655	2R_6622655_INS [dm3] 2R_10735150_INS [dm6]	A	AACTTGTGCAACCGTGAAAG...	3.719e^-5	0.878	UPSTREAM CG7220 INTRON CG7220
3L	9130308	3L_9130308_SNP [dm3] 3L_9137208_SNP [dm6]	T	C	3.751e^-5	0.878	UPSTREAM nwk & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
X	21207647	X_21207647_DEL [dm3] X_21336620_DEL [dm6]	TTGGAAATTATTG...	AAAAA	3.775e^-5	0.878	INTRON tty
3R	24469790	3R_24469790_SNP [dm3] 3R_28644068_SNP [dm6]	A	G	3.823e^-5	0.878	INTERGENIC
2R	9789533	2R_9789533_SNP [dm3] 2R_13902028_SNP [dm6]	A	T	3.944e^-5	0.878	SYNONYMOUS_CODING shot	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	10061566	2L_10061566_SNP [dm3] 2L_10061566_SNP [dm6]	G	C	4.015e^-5	0.878	INTRON Spn31A
3L	10802715	3L_10802715_SNP [dm3] 3L_10809615_SNP [dm6]	A	C	4.046e^-5	0.878	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	16060378	3R_16060378_SNP [dm3] 3R_20234656_SNP [dm6]	C	T	4.128e^-5	0.878	INTRON Nlg4
X	20406098	X_20406098_SNP [dm3] X_20535071_SNP [dm6]	T	C	4.216e^-5	0.878	INTERGENIC
3L	14433920	3L_14433920_SNP [dm3] 3L_14440820_SNP [dm6]	T	G	4.242e^-5	0.878	INTRON bbg
3L	4382190	3L_4382190_SNP [dm3] 3L_4382190_SNP [dm6]	G	C	4.248e^-5	0.878	UPSTREAM CG32240 INTERGENIC
3L	10802725	3L_10802725_SNP [dm3] 3L_10809625_SNP [dm6]	C	T	4.262e^-5	0.878	INTERGENIC
3L	17978963	3L_17978963_SNP [dm3] 3L_17985863_SNP [dm6]	G	A	4.316e^-5	0.878	INTRON Eip75B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	13632652	2L_13632652_SNP [dm3] 2L_13632652_SNP [dm6]	T	A	4.358e^-5	0.878	DOWNSTREAM CR43410 INTRON kuz
X	20405950	X_20405950_SNP [dm3] X_20534923_SNP [dm6]	G	C	4.389e^-5	0.878	INTERGENIC
3L	2856152	3L_2856152_SNP [dm3] 3L_2856152_SNP [dm6]	C	G	4.499e^-5	0.878	INTRON CG43444
X	13904703	X_13904703_SNP [dm3] X_14010670_SNP [dm6]	T	A	4.561e^-5	0.878	INTERGENIC
X	3385990	X_3385990_SNP [dm3] X_3491957_SNP [dm6]	G	A	4.595e^-5	0.878	SYNONYMOUS_CODING Gas8 INTRON CR44999	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA
3R	6833206	3R_6833206_SNP [dm3] 3R_11007484_SNP [dm6]	A	G	4.736e^-5	0.878	INTRON CG34114	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	5481087	3R_5481087_SNP [dm3] 3R_9655365_SNP [dm6]	A	C	4.774e^-5	0.878	INTRON CG9492	TF binding site mE1_TFBS_chinmo
X	12181760	X_12181760_SNP [dm3] X_12287727_SNP [dm6]	A	G	4.884e^-5	0.878	INTRON Ten-a
2R	15228543	2R_15228543_SNP [dm3] 2R_19341038_SNP [dm6]	T	A	4.904e^-5	0.878	UPSTREAM CG9975 INTRON Rgk1
3R	26456909	3R_26456909_SNP [dm3] 3R_30631187_SNP [dm6]	G	T	4.952e^-5	0.878	INTERGENIC	TF binding site mE1_TFBS_cad
2R	9789530	2R_9789530_SNP [dm3] 2R_13902025_SNP [dm6]	T	C	4.957e^-5	0.878	SYNONYMOUS_CODING shot	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	9116213	3R_9116213_SNP [dm3] 3R_13290491_SNP [dm6]	A	T	4.960e^-5	0.878	UPSTREAM Osi22 INTERGENIC
3R	7408051	3R_7408051_SNP [dm3] 3R_11582329_SNP [dm6]	G	A	5.014e^-5	0.878	UPSTREAM wkd DOWNSTREAM CG5342 INTRON wkd	TF binding site BDTNP1_TFBS_dl
3R	18132155	3R_18132155_SNP [dm3] 3R_22306433_SNP [dm6]	G	T	5.169e^-5	0.878	INTERGENIC
3R	11715538	3R_11715538_SNP [dm3] 3R_15889816_SNP [dm6]	A	G	5.209e^-5	0.878	SYNONYMOUS_CODING CG14877
2L	1185242	2L_1185242_SNP [dm3] 2L_1185242_SNP [dm6]	C	T	5.225e^-5	0.878	SYNONYMOUS_CODING Tgt UPSTREAM CG5001	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	7271559	2L_7271559_SNP [dm3] 2L_7271559_SNP [dm6]	G	C	5.247e^-5	0.878	INTRON Wnt4	TF binding site mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
X	1936957	X_1936957_SNP [dm3] X_2042924_SNP [dm6]	G	C	5.248e^-5	0.878	UTR_3_PRIME CG4325 UPSTREAM Actn & 1 other DOWNSTREAM CG4325 INTRON CG4313	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb
2L	12086489	2L_12086489_SNP [dm3] 2L_12086489_SNP [dm6]	T	A	5.256e^-5	0.878	UPSTREAM CR44593 & 1 other DOWNSTREAM CR44592 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad
3R	10701935	3R_10701935_SNP [dm3] 3R_14876213_SNP [dm6]	G	A	5.426e^-5	0.878	UPSTREAM btsz INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	13439845	2L_13439845_SNP [dm3] 2L_13439845_SNP [dm6]	T	A	5.427e^-5	0.878	UTR_3_PRIME Tehao DOWNSTREAM Tehao INTRON CG42784 EXON CR45683
2L	10548500	2L_10548500_SNP [dm3] 2L_10548500_SNP [dm6]	A	T	5.496e^-5	0.878	INTRON Trim9	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	18132145	3R_18132145_SNP [dm3] 3R_22306423_SNP [dm6]	T	G	5.536e^-5	0.878	INTERGENIC
2R	14559167	2R_14559167_SNP [dm3] 2R_18671662_SNP [dm6]	T	C	5.573e^-5	0.878	INTRON edl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15064270	2R_15064270_SNP [dm3] 2R_19176765_SNP [dm6]	T	C	5.672e^-5	0.878	INTRON CG10737
2R	18376506	2R_18376506_SNP [dm3] 2R_22489001_SNP [dm6]	G	A	5.676e^-5	0.878	SYNONYMOUS_CODING CG4554	TF binding site mE1_TFBS_cad

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By genomic position
Variant impact
Gene name

mn_Triglyceri_LoDiet phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results