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=1.956e^-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	0.09997
In_2R_NS	0.09765

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	5.451	0.0655

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2170 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
2L	14109774	2L_14109774_SNP [dm3] 2L_14109774_SNP [dm6]	G	T	9.375e^-8	0.176	SYNONYMOUS_CODING CG31769 UPSTREAM CG15293
2L	14111029	2L_14111029_SNP [dm3] 2L_14111029_SNP [dm6]	G	A	1.483e^-6	0.714	UPSTREAM CG31769 INTERGENIC
2L	6605766	2L_6605766_SNP [dm3] 2L_6605766_SNP [dm6]	T	C	2.701e^-6	0.714	INTERGENIC
X	12603563	X_12603563_SNP [dm3] X_12709530_SNP [dm6]	C	T	2.873e^-6	0.714	DOWNSTREAM CG15725 INTRON Smr
3L	5266323	3L_5266323_SNP [dm3] 3L_5273223_SNP [dm6]	T	A	2.885e^-6	0.714	UTR_5_PRIME shep INTRON shep
3L	2552127	3L_2552127_SNP [dm3] 3L_2552127_SNP [dm6]	A	C	4.300e^-6	0.714	INTRON Spn
2R	15064256	2R_15064256_SNP [dm3] 2R_19176751_SNP [dm6]	T	C	4.586e^-6	0.714	SPLICE_SITE_REGION CG10737 INTRON CG10737
3L	10981177	3L_10981177_SNP [dm3] 3L_10988077_SNP [dm6]	A	G	4.712e^-6	0.714	INTRON klu
3R	12371552	3R_12371552_SNP [dm3] 3R_16545830_SNP [dm6]	G	T	5.296e^-6	0.714	INTRON CG42342	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
X	12721668	X_12721668_SNP [dm3] X_12827635_SNP [dm6]	T	C	5.814e^-6	0.714	INTRON Pde9
2R	6861309	2R_6861309_SNP [dm3] 2R_10973804_SNP [dm6]	G	A	5.969e^-6	0.714	INTERGENIC
X	20361541	X_20361541_SNP [dm3] X_20490514_SNP [dm6]	T	G	6.773e^-6	0.714	INTRON RhoGAP19D	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14110235	2L_14110235_SNP [dm3] 2L_14110235_SNP [dm6]	A	G	7.217e^-6	0.714	NON_SYNONYMOUS_CODING CG31769 UPSTREAM CG15293
3L	9084737	3L_9084737_DEL [dm3] 3L_9091637_DEL [dm6]	TTAGGCT	T	7.430e^-6	0.714	INTRON Tequila
X	8928028	X_8928028_SNP [dm3] X_9033995_SNP [dm6]	T	A	7.724e^-6	0.714	INTRON CR43836 & 1 other
X	5228646	X_5228646_SNP [dm3] X_5334613_SNP [dm6]	G	A	8.095e^-6	0.714	DOWNSTREAM CanB INTERGENIC
2L	7953695	2L_7953695_SNP [dm3] 2L_7953695_SNP [dm6]	C	T	8.475e^-6	0.714	INTRON Snoo
2R	15064281	2R_15064281_SNP [dm3] 2R_19176776_SNP [dm6]	T	C	8.900e^-6	0.714	INTRON CG10737
3L	17553473	3L_17553473_SNP [dm3] 3L_17560373_SNP [dm6]	A	T	8.960e^-6	0.714	UTR_3_PRIME Eip74EF
2R	19823898	2R_19823898_SNP [dm3] 2R_23936375_SNP [dm6]	A	G	9.299e^-6	0.714	UPSTREAM Ca-P60A DOWNSTREAM CG3735 INTERGENIC
X	12603566	X_12603566_SNP [dm3] X_12709533_SNP [dm6]	G	A	9.307e^-6	0.714	DOWNSTREAM CG15725 INTRON Smr
3L	21772932	3L_21772932_SNP [dm3] 3L_21779832_SNP [dm6]	A	G	9.338e^-6	0.714	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	17533902	3L_17533902_SNP [dm3] 3L_17540802_SNP [dm6]	T	G	9.398e^-6	0.714	SYNONYMOUS_CODING Nedd4
3L	6000523	3L_6000523_SNP [dm3] 3L_6007423_SNP [dm6]	T	C	9.789e^-6	0.714	INTRON PVRAP
X	16523876	X_16523876_SNP [dm3] X_16629843_SNP [dm6]	G	T	1.056e^-5	0.714	SYNONYMOUS_CODING Rok DOWNSTREAM CG9777	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	14114851	2L_14114851_SNP [dm3] 2L_14114851_SNP [dm6]	G	A	1.078e^-5	0.714	INTERGENIC
2L	7161861	2L_7161861_SNP [dm3] 2L_7161861_SNP [dm6]	A	C	1.114e^-5	0.714	INTERGENIC
3R	23988616	3R_23988616_SNP [dm3] 3R_28162894_SNP [dm6]	C	A	1.149e^-5	0.714	INTRON CG34354
2R	3197264	2R_3197264_SNP [dm3] 2R_7309759_SNP [dm6]	G	A	1.174e^-5	0.714	INTERGENIC
2L	6604030	2L_6604030_SNP [dm3] 2L_6604030_SNP [dm6]	A	T	1.192e^-5	0.714	INTERGENIC
2R	13526944	2R_13526944_DEL [dm3] 2R_17639439_DEL [dm6]	TGGTTTATTTACATT...	T	1.212e^-5	0.714	UPSTREAM CG10936 INTERGENIC	TF binding site mE1_TFBS_Trl
X	8928258	X_8928258_SNP [dm3] X_9034225_SNP [dm6]	G	T	1.311e^-5	0.714	INTRON CR43836 & 1 other
2L	14113502	2L_14113502_SNP [dm3] 2L_14113502_SNP [dm6]	A	C	1.357e^-5	0.714	INTERGENIC
X	9689979	X_9689979_SNP [dm3] X_9795946_SNP [dm6]	T	C	1.373e^-5	0.714	INTRON CG32698
3L	12836828	3L_12836828_SNP [dm3] 3L_12843728_SNP [dm6]	T	G	1.400e^-5	0.714	UPSTREAM CG10960 DOWNSTREAM CG10948 INTERGENIC
X	20361348	X_20361348_SNP [dm3] X_20490321_SNP [dm6]	T	G	1.420e^-5	0.714	INTRON RhoGAP19D	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_dl
2L	7953836	2L_7953836_SNP [dm3] 2L_7953836_SNP [dm6]	G	T	1.426e^-5	0.714	INTRON Snoo
2L	7160904	2L_7160904_SNP [dm3] 2L_7160904_SNP [dm6]	A	G	1.459e^-5	0.714	INTERGENIC
2L	14226156	2L_14226156_SNP [dm3] 2L_14226156_SNP [dm6]	A	T	1.486e^-5	0.714	INTRON Dyrk2	TF binding site BDTNP1_TFBS_da
3L	14660407	3L_14660407_SNP [dm3] 3L_14667307_SNP [dm6]	A	G	1.584e^-5	0.723	SYNONYMOUS_CODING dlp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15064258	2R_15064258_SNP [dm3] 2R_19176753_SNP [dm6]	C	T	1.627e^-5	0.723	INTRON CG10737
2R	9601281	2R_9601281_SNP [dm3] 2R_13713776_SNP [dm6]	A	G	1.642e^-5	0.723	SYNONYMOUS_CODING fas
3L	5289878	3L_5289878_SNP [dm3] 3L_5296778_SNP [dm6]	T	C	1.716e^-5	0.723	INTERGENIC
3L	6769271	3L_6769271_SNP [dm3] 3L_6776171_SNP [dm6]	T	C	1.766e^-5	0.723	INTERGENIC
X	8928277	X_8928277_SNP [dm3] X_9034244_SNP [dm6]	A	G	1.766e^-5	0.723	INTRON CR43836 & 1 other
3L	1454382	3L_1454382_INS [dm3] 3L_1454382_INS [dm6]	T	TT	1.785e^-5	0.723	INTRON Ptp61F	TF binding site BDTNP1_TFBS_twi
3R	19505733	3R_19505733_SNP [dm3] 3R_23680011_SNP [dm6]	G	A	1.814e^-5	0.723	UPSTREAM eIF-3p66 DOWNSTREAM CG10157 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
3L	17533878	3L_17533878_SNP [dm3] 3L_17540778_SNP [dm6]	T	C	1.988e^-5	0.73	SYNONYMOUS_CODING Nedd4
X	8928257	X_8928257_SNP [dm3] X_9034224_SNP [dm6]	T	A	1.994e^-5	0.73	INTRON CR43836 & 1 other
3R	12859312	3R_12859312_SNP [dm3] 3R_17033590_SNP [dm6]	A	G	2.122e^-5	0.73	UTR_3_PRIME CG4009 DOWNSTREAM CG4009 & 1 other
3L	5245238	3L_5245238_SNP [dm3] 3L_5252138_SNP [dm6]	A	C	2.195e^-5	0.73	INTRON shep
3R	12859328	3R_12859328_SNP [dm3] 3R_17033606_SNP [dm6]	T	A	2.253e^-5	0.73	UTR_3_PRIME CG4009 DOWNSTREAM CG4009 & 1 other
3L	5245239	3L_5245239_SNP [dm3] 3L_5252139_SNP [dm6]	T	A	2.278e^-5	0.73	INTRON shep
2L	14116203	2L_14116203_SNP [dm3] 2L_14116203_SNP [dm6]	A	T	2.356e^-5	0.73	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14723070	2L_14723070_SNP [dm3] 2L_14723070_SNP [dm6]	T	G	2.364e^-5	0.73	INTERGENIC
X	20361327	X_20361327_SNP [dm3] X_20490300_SNP [dm6]	C	A	2.414e^-5	0.73	INTRON RhoGAP19D	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_dl
2L	14139082	2L_14139082_SNP [dm3] 2L_14139082_SNP [dm6]	T	C	2.448e^-5	0.73	INTRON CG17341
X	4788228	X_4788228_SNP [dm3] X_4894195_SNP [dm6]	C	A	2.458e^-5	0.73	INTRON CG42594
X	9689759	X_9689759_SNP [dm3] X_9795726_SNP [dm6]	T	A	2.510e^-5	0.73	INTRON CG32698
3L	4410480	3L_4410480_SNP [dm3] 3L_4410480_SNP [dm6]	C	T	2.536e^-5	0.73	INTRON DOR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Trl
X	8928049	X_8928049_SNP [dm3] X_9034016_SNP [dm6]	T	G	2.557e^-5	0.73	INTRON CR43836 & 1 other
X	8928195	X_8928195_SNP [dm3] X_9034162_SNP [dm6]	C	T	2.557e^-5	0.73	INTRON CR43836 & 1 other
2L	14101553	2L_14101553_SNP [dm3] 2L_14101553_SNP [dm6]	A	T	2.633e^-5	0.73	INTERGENIC
3L	1673372	3L_1673372_SNP [dm3] 3L_1673372_SNP [dm6]	A	T	2.707e^-5	0.73	UPSTREAM CG13930 INTERGENIC
3L	19497545	3L_19497545_SNP [dm3] 3L_19504445_SNP [dm6]	C	T	2.804e^-5	0.73	UPSTREAM CG9452 DOWNSTREAM CR45731 INTERGENIC
3L	1454379	3L_1454379_SNP [dm3] 3L_1454379_SNP [dm6]	T	A	2.826e^-5	0.73	INTRON Ptp61F	TF binding site BDTNP1_TFBS_twi
2L	14226191	2L_14226191_DEL [dm3] 2L_14226191_DEL [dm6]	TT	T	2.871e^-5	0.73	INTRON Dyrk2	TF binding site BDTNP1_TFBS_da
X	5287638	X_5287638_SNP [dm3] X_5393605_SNP [dm6]	A	T	2.919e^-5	0.73	INTRON SK
3R	13738705	3R_13738705_SNP [dm3] 3R_17912983_SNP [dm6]	G	C	2.959e^-5	0.73	DOWNSTREAM CG43445 INTRON Rim
X	15452793	X_15452793_SNP [dm3] X_15558760_SNP [dm6]	C	A	2.994e^-5	0.73	INTERGENIC
2L	9553752	2L_9553752_SNP [dm3] 2L_9553752_SNP [dm6]	C	A	2.994e^-5	0.73	INTRON jp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	9649237	2L_9649237_SNP [dm3] 2L_9649237_SNP [dm6]	T	G	2.997e^-5	0.73	SYNONYMOUS_CODING Apoltp
X	21861771	X_21861771_SNP [dm3] X_22459935_SNP [dm6]	G	A	3.027e^-5	0.73	INTRON CG14619	transposable element FlyBase
X	12174953	X_12174953_SNP [dm3] X_12280920_SNP [dm6]	C	G	3.051e^-5	0.73	INTRON Ten-a
3L	5245142	3L_5245142_SNP [dm3] 3L_5252042_SNP [dm6]	A	T	3.135e^-5	0.73	INTRON shep
2R	15064270	2R_15064270_SNP [dm3] 2R_19176765_SNP [dm6]	T	C	3.148e^-5	0.73	INTRON CG10737
3L	2595088	3L_2595088_SNP [dm3] 3L_2595088_SNP [dm6]	C	T	3.151e^-5	0.73	UTR_3_PRIME dos UPSTREAM CG16984 DOWNSTREAM CG12182	TF binding site mE1_TFBS_cad
2R	19914154	2R_19914154_SNP [dm3] 2R_24026631_SNP [dm6]	C	A	3.242e^-5	0.73	UPSTREAM PebIII & 1 other DOWNSTREAM Adk2 INTRON PebIII	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	15210888	3L_15210888_SNP [dm3] 3L_15217788_SNP [dm6]	C	T	3.312e^-5	0.73	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	12975855	2L_12975855_SNP [dm3] 2L_12975855_SNP [dm6]	T	A	3.321e^-5	0.73	INTRON Vha68-2
2L	5890101	2L_5890101_SNP [dm3] 2L_5890101_SNP [dm6]	G	A	3.367e^-5	0.73	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5890104	2L_5890104_SNP [dm3] 2L_5890104_SNP [dm6]	T	C	3.367e^-5	0.73	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	3477973	2L_3477973_SNP [dm3] 2L_3477973_SNP [dm6]	A	C	3.457e^-5	0.73	UPSTREAM Thor DOWNSTREAM CR43928 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	9649280	2L_9649280_SNP [dm3] 2L_9649280_SNP [dm6]	T	C	3.475e^-5	0.73	SYNONYMOUS_CODING Apoltp
2L	7161881	2L_7161881_SNP [dm3] 2L_7161881_SNP [dm6]	C	A	3.520e^-5	0.73	INTERGENIC
3L	11255359	3L_11255359_SNP [dm3] 3L_11262259_SNP [dm6]	T	G	3.538e^-5	0.73	INTERGENIC	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 mE1_TFBS_HSA
2R	7328385	2R_7328385_SNP [dm3] 2R_11440880_SNP [dm6]	C	A	3.551e^-5	0.73	INTRON CG7777
X	20402304	X_20402304_SNP [dm3] X_20531277_SNP [dm6]	T	A	3.568e^-5	0.73	INTERGENIC
2R	18859948	2R_18859948_SNP [dm3] 2R_22972425_SNP [dm6]	A	T	3.579e^-5	0.73	INTERGENIC	TF binding site mE1_TFBS_chinmo
X	17366929	X_17366929_SNP [dm3] X_17472896_SNP [dm6]	G	A	3.641e^-5	0.73	INTRON CG43658	TF binding site mE1_TFBS_cad
X	16377217	X_16377217_INS [dm3] X_16483184_INS [dm6]	T	TGTT	3.704e^-5	0.73	INTRON para
X	21832019	X_21832019_SNP [dm3] X_22430184_SNP [dm6]	A	G	3.882e^-5	0.73	INTERGENIC	transposable element FlyBase
2L	5630378	2L_5630378_DEL [dm3] 2L_5630378_DEL [dm6]	CCTTTAAGCATCTGAGT...	A	3.920e^-5	0.73	INTRON CG31646	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_chinmo
3R	12859346	3R_12859346_SNP [dm3] 3R_17033624_SNP [dm6]	C	T	3.940e^-5	0.73	UTR_3_PRIME CG4009 DOWNSTREAM CG4009 & 1 other
2L	14133695	2L_14133695_SNP [dm3] 2L_14133695_SNP [dm6]	A	T	3.947e^-5	0.73	UPSTREAM CG17341 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11308832	3L_11308832_SNP [dm3] 3L_11315732_SNP [dm6]	T	A	3.952e^-5	0.73	EXON CR44361
3L	1282259	3L_1282259_SNP [dm3] 3L_1282259_SNP [dm6]	G	A	3.960e^-5	0.73	INTRON CG32333
3L	6769300	3L_6769300_SNP [dm3] 3L_6776200_SNP [dm6]	T	C	4.014e^-5	0.73	INTERGENIC
X	16136625	X_16136625_SNP [dm3] X_16242592_SNP [dm6]	T	A	4.056e^-5	0.73	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	7874948	3R_7874948_SNP [dm3] 3R_12049226_SNP [dm6]	G	T	4.086e^-5	0.73	UPSTREAM CG14739 INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

PC2_Nutri_Score_Low phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results