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=2.386e^-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_2R_NS	5.9894	0.0501

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2168 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
3R	10359904	3R_10359904_SNP [dm3] 3R_14534182_SNP [dm6]	G	A	5.669e^-7	0.488	INTRON Pde6
3R	25956440	3R_25956440_SNP [dm3] 3R_30130718_SNP [dm6]	A	C	1.475e^-6	0.488	SYNONYMOUS_CODING CG31029	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3R	25953010	3R_25953010_SNP [dm3] 3R_30127288_SNP [dm6]	A	G	1.607e^-6	0.488	NON_SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	15899551	3L_15899551_SNP [dm3] 3L_15906451_SNP [dm6]	T	C	1.732e^-6	0.488	INTRON sff
3R	25953104	3R_25953104_SNP [dm3] 3R_30127382_SNP [dm6]	A	T	1.993e^-6	0.488	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	11217493	3R_11217493_SNP [dm3] 3R_15391771_SNP [dm6]	C	T	2.811e^-6	0.488	INTRON Rbp	TF binding site mE1_TFBS_cad
3R	25953203	3R_25953203_SNP [dm3] 3R_30127481_SNP [dm6]	A	G	3.468e^-6	0.488	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	25952966	3R_25952966_SNP [dm3] 3R_30127244_SNP [dm6]	T	C	4.090e^-6	0.488	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	17462108	2R_17462108_SNP [dm3] 2R_21574603_SNP [dm6]	C	T	4.181e^-6	0.488	INTRON CG10440
3R	25952830	3R_25952830_SNP [dm3] 3R_30127108_SNP [dm6]	T	C	4.309e^-6	0.488	NON_SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23253202	3R_23253202_SNP [dm3] 3R_27427480_SNP [dm6]	C	T	4.389e^-6	0.488	INTRON side
3L	11357121	3L_11357121_SNP [dm3] 3L_11364021_SNP [dm6]	G	T	4.698e^-6	0.488	UPSTREAM CR45036 INTRON CG6163	TF binding site mE1_TFBS_cad
2R	7497535	2R_7497535_SNP [dm3] 2R_11610030_SNP [dm6]	C	A	4.980e^-6	0.488	INTRON tou	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	13722301	3R_13722301_SNP [dm3] 3R_17896579_SNP [dm6]	T	A	5.006e^-6	0.488	INTRON Rim
3R	10360251	3R_10360251_SNP [dm3] 3R_14534529_SNP [dm6]	T	C	5.052e^-6	0.488	INTRON Pde6
3R	11323756	3R_11323756_SNP [dm3] 3R_15498034_SNP [dm6]	T	G	5.085e^-6	0.488	INTERGENIC
3L	551351	3L_551351_SNP [dm3] 3L_551351_SNP [dm6]	A	G	5.354e^-6	0.488	INTRON hipk	TF binding site BDTNP1_TFBS_dl
3L	11488657	3L_11488657_SNP [dm3] 3L_11495557_SNP [dm6]	C	A	5.433e^-6	0.488	UTR_3_PRIME chrb	TF binding site mE1_TFBS_HSA mE1_TFBS_ttk
3R	25953305	3R_25953305_SNP [dm3] 3R_30127583_SNP [dm6]	A	G	5.935e^-6	0.488	SYNONYMOUS_CODING Ppi1	TF binding site mE1_TFBS_chinmo
2R	18455202	2R_18455202_SNP [dm3] 2R_22567697_SNP [dm6]	C	T	6.223e^-6	0.488	INTRON dnr1
X	5877626	X_5877626_SNP [dm3] X_5983593_SNP [dm6]	C	T	6.310e^-6	0.488	INTRON Grip
3R	22934976	3R_22934976_SNP [dm3] 3R_27109254_SNP [dm6]	A	G	6.598e^-6	0.488	SYNONYMOUS_CODING gb UPSTREAM CR45209
3R	5443035	3R_5443035_SNP [dm3] 3R_9617313_SNP [dm6]	A	G	6.812e^-6	0.488	INTRON CG8312
2L	3271697	2L_3271697_SNP [dm3] 2L_3271697_SNP [dm6]	A	T	7.204e^-6	0.488	UTR_3_PRIME CG3347
3L	941551	3L_941551_SNP [dm3] 3L_941551_SNP [dm6]	A	G	7.281e^-6	0.488	INTRON Glut1
2L	2247949	2L_2247949_DEL [dm3] 2L_2247949_DEL [dm6]	GC	G	7.675e^-6	0.488	DOWNSTREAM CR42859 INTERGENIC
3R	11443794	3R_11443794_INS [dm3] 3R_15618072_INS [dm6]	A	AA	7.695e^-6	0.488	INTERGENIC
3R	9153967	3R_9153967_SNP [dm3] 3R_13328245_SNP [dm6]	A	G	8.300e^-6	0.488	DOWNSTREAM PK2-R2 INTERGENIC
X	19765726	X_19765726_SNP [dm3] X_19871693_SNP [dm6]	G	T	8.381e^-6	0.488	INTRON Hers	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	13722160	3R_13722160_SNP [dm3] 3R_17896438_SNP [dm6]	T	A	8.472e^-6	0.488	INTRON Rim
2R	18455229	2R_18455229_SNP [dm3] 2R_22567724_SNP [dm6]	C	A	8.634e^-6	0.488	INTRON dnr1
3L	11191888	3L_11191888_SNP [dm3] 3L_11198788_SNP [dm6]	A	G	8.812e^-6	0.488	SYNONYMOUS_CODING Plod UPSTREAM CG7607	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	13232326	2L_13232326_SNP [dm3] 2L_13232326_SNP [dm6]	T	C	8.851e^-6	0.488	SYNONYMOUS_CODING Prosalpha6T	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	4511204	3L_4511204_SNP [dm3] 3L_4511204_SNP [dm6]	C	T	8.856e^-6	0.488	UTR_3_PRIME Tie	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
3R	14987341	3R_14987341_SNP [dm3] 3R_19161619_SNP [dm6]	G	C	9.276e^-6	0.497	SYNONYMOUS_CODING CG42359 INTRON CG42358	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_sens
3R	20931584	3R_20931584_SNP [dm3] 3R_25105862_SNP [dm6]	G	A	1.070e^-5	0.545	SYNONYMOUS_CODING CG34027
3L	8751097	3L_8751097_SNP [dm3] 3L_8757997_SNP [dm6]	G	A	1.077e^-5	0.545	DOWNSTREAM CG6576 INTRON Fhos
3R	11160926	3R_11160926_SNP [dm3] 3R_15335204_SNP [dm6]	C	T	1.139e^-5	0.548	SYNONYMOUS_CODING Sra-1	TF binding site mE1_TFBS_chinmo
3R	21341198	3R_21341198_SNP [dm3] 3R_25515476_SNP [dm6]	A	C	1.141e^-5	0.548	UPSTREAM msi INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	4510238	3L_4510238_SNP [dm3] 3L_4510238_SNP [dm6]	T	A	1.291e^-5	0.605	DOWNSTREAM Tie INTERGENIC
3L	16055724	3L_16055724_SNP [dm3] 3L_16062624_SNP [dm6]	C	T	1.391e^-5	0.621	SYNONYMOUS_CODING Mbs
3R	21341184	3R_21341184_SNP [dm3] 3R_25515462_SNP [dm6]	T	C	1.410e^-5	0.621	UPSTREAM msi INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	4510231	3L_4510231_SNP [dm3] 3L_4510231_SNP [dm6]	A	G	1.476e^-5	0.621	DOWNSTREAM Tie INTERGENIC
3L	20425634	3L_20425634_SNP [dm3] 3L_20432534_SNP [dm6]	T	A	1.484e^-5	0.621	UTR_5_PRIME Psn UPSTREAM Psn & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
3L	20425790	3L_20425790_SNP [dm3] 3L_20432690_SNP [dm6]	T	C	1.490e^-5	0.621	UTR_5_PRIME Psn UPSTREAM Las	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx
2R	7504304	2R_7504304_SNP [dm3] 2R_11616799_SNP [dm6]	C	G	1.549e^-5	0.628	UPSTREAM tou DOWNSTREAM Egm & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sbb mE1_TFBS_Trl
3R	23268755	3R_23268755_SNP [dm3] 3R_27443033_SNP [dm6]	T	C	1.629e^-5	0.628	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23252659	3R_23252659_SNP [dm3] 3R_27426937_SNP [dm6]	T	A	1.639e^-5	0.628	INTRON side
3R	5449451	3R_5449451_SNP [dm3] 3R_9623729_SNP [dm6]	T	C	1.678e^-5	0.628	SYNONYMOUS_CODING CG8312	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23268180	3R_23268180_SNP [dm3] 3R_27442458_SNP [dm6]	T	A	1.690e^-5	0.628	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_eve mE1_TFBS_HSA mE1_TFBS_sens
3R	17965732	3R_17965732_SNP [dm3] 3R_22140010_SNP [dm6]	C	A	1.770e^-5	0.628	INTRON SKIP	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	4245104	X_4245104_SNP [dm3] X_4351071_SNP [dm6]	A	T	1.773e^-5	0.628	INTRON norpA
3R	16064229	3R_16064229_SNP [dm3] 3R_20238507_SNP [dm6]	A	T	1.794e^-5	0.628	INTRON Nlg4
3L	7865777	3L_7865777_SNP [dm3] 3L_7872677_SNP [dm6]	A	G	1.828e^-5	0.628	INTRON CG32365	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
3R	23252573	3R_23252573_SNP [dm3] 3R_27426851_SNP [dm6]	C	T	1.841e^-5	0.628	INTRON side
3L	3487801	3L_3487801_SNP [dm3] 3L_3487801_SNP [dm6]	C	T	1.936e^-5	0.629	INTRON CG42324
3R	11161151	3R_11161151_SNP [dm3] 3R_15335429_SNP [dm6]	G	A	1.957e^-5	0.629	SYNONYMOUS_CODING Sra-1	TF binding site mE1_TFBS_sens
3L	4510259	3L_4510259_SNP [dm3] 3L_4510259_SNP [dm6]	T	C	1.996e^-5	0.629	DOWNSTREAM Tie INTERGENIC
2R	9949237	2R_9949237_SNP [dm3] 2R_14061732_SNP [dm6]	A	T	2.014e^-5	0.629	UTR_3_PRIME Prosap
3L	11357109	3L_11357109_INS [dm3] 3L_11364009_INS [dm6]	A	ACAA	2.014e^-5	0.629	UPSTREAM CR45036 INTRON CG6163	TF binding site mE1_TFBS_cad
2L	3261343	2L_3261343_SNP [dm3] 2L_3261343_SNP [dm6]	C	T	2.197e^-5	0.664	UPSTREAM CR45337 DOWNSTREAM CR45338 INTERGENIC
X	9791472	X_9791472_DEL [dm3] X_9897439_DEL [dm6]	CAATTGAC	C	2.258e^-5	0.664	INTRON CG15249
3R	22938002	3R_22938002_SNP [dm3] 3R_27112280_SNP [dm6]	G	A	2.295e^-5	0.664	UPSTREAM CG5815 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA
3R	25956593	3R_25956593_SNP [dm3] 3R_30130871_SNP [dm6]	G	T	2.328e^-5	0.664	SYNONYMOUS_CODING CG31029	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	11519565	2R_11519565_SNP [dm3] 2R_15632060_SNP [dm6]	T	C	2.332e^-5	0.664	INTRON CG42524
3R	14175484	3R_14175484_SNP [dm3] 3R_18349762_SNP [dm6]	T	C	2.389e^-5	0.664	INTRON CG15803
2L	4076112	2L_4076112_SNP [dm3] 2L_4076112_SNP [dm6]	C	G	2.400e^-5	0.664	UPSTREAM CR44984 INTRON ed
3L	6653492	3L_6653492_SNP [dm3] 3L_6660392_SNP [dm6]	A	C	2.429e^-5	0.664	INTERGENIC
3L	15863160	3L_15863160_SNP [dm3] 3L_15870060_SNP [dm6]	C	T	2.444e^-5	0.664	SYNONYMOUS_CODING pHCl	TF binding site mE1_TFBS_cad
3L	941596	3L_941596_SNP [dm3] 3L_941596_SNP [dm6]	T	A	2.486e^-5	0.666	INTRON Glut1
2L	6310982	2L_6310982_SNP [dm3] 2L_6310982_SNP [dm6]	T	C	2.601e^-5	0.687	INTRON Ddr
2L	17519408	2L_17519408_SNP [dm3] 2L_17519408_SNP [dm6]	C	T	2.777e^-5	0.718	SYNONYMOUS_CODING Dhc36C	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	7499416	2R_7499416_INS [dm3] 2R_11611911_INS [dm6]	G	GA	2.796e^-5	0.718	INTRON tou	TF binding site BDTNP1_TFBS_dl
3L	15900103	3L_15900103_SNP [dm3] 3L_15907003_SNP [dm6]	T	C	2.987e^-5	0.736	INTRON sff
3R	20314461	3R_20314461_SNP [dm3] 3R_24488739_SNP [dm6]	T	A	3.009e^-5	0.736	DOWNSTREAM mir-1017 INTRON nAChRalpha2
2L	2619347	2L_2619347_SNP [dm3] 2L_2619347_SNP [dm6]	A	T	3.063e^-5	0.736	UPSTREAM CG43403 INTERGENIC
3R	22947316	3R_22947316_SNP [dm3] 3R_27121594_SNP [dm6]	T	C	3.069e^-5	0.736	DOWNSTREAM CG6059 & 1 other INTERGENIC
3L	11357310	3L_11357310_SNP [dm3] 3L_11364210_SNP [dm6]	G	A	3.094e^-5	0.736	UPSTREAM CR45036 INTRON CG6163
3R	13589972	3R_13589972_SNP [dm3] 3R_17764250_SNP [dm6]	C	T	3.138e^-5	0.736	INTERGENIC
3L	15855622	3L_15855622_SNP [dm3] 3L_15862522_SNP [dm6]	G	T	3.173e^-5	0.736	DOWNSTREAM pHCl INTRON pHCl
X	5877684	X_5877684_SNP [dm3] X_5983651_SNP [dm6]	A	T	3.180e^-5	0.736	INTRON Grip
3R	26106219	3R_26106219_SNP [dm3] 3R_30280497_SNP [dm6]	G	A	3.305e^-5	0.745	INTRON hdc
3L	15837750	3L_15837750_SNP [dm3] 3L_15844650_SNP [dm6]	G	T	3.329e^-5	0.745	UPSTREAM CG32150 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	6311047	2L_6311047_SNP [dm3] 2L_6311047_SNP [dm6]	G	A	3.339e^-5	0.745	INTRON Ddr
2R	9965586	2R_9965586_SNP [dm3] 2R_14078081_SNP [dm6]	T	C	3.426e^-5	0.753	INTRON Prosap
3L	6652430	3L_6652430_SNP [dm3] 3L_6659330_SNP [dm6]	T	C	3.455e^-5	0.753	INTERGENIC
3R	17924047	3R_17924047_SNP [dm3] 3R_22098325_SNP [dm6]	C	T	3.619e^-5	0.78	INTRON CG5778
X	8415712	X_8415712_SNP [dm3] X_8521679_SNP [dm6]	A	C	3.764e^-5	0.78	INTRON Nrg
3L	15899108	3L_15899108_SNP [dm3] 3L_15906008_SNP [dm6]	T	C	3.852e^-5	0.78	SYNONYMOUS_CODING sff
2L	10185439	2L_10185439_SNP [dm3] 2L_10185439_SNP [dm6]	C	T	3.866e^-5	0.78	INTRON Sur	TF binding site mE1_TFBS_inv
3L	7486056	3L_7486056_SNP [dm3] 3L_7492956_SNP [dm6]	T	G	3.954e^-5	0.78	NON_SYNONYMOUS_CODING Cyp316a1 DOWNSTREAM Cyp4d8
X	8163625	X_8163625_SNP [dm3] X_8269592_SNP [dm6]	G	A	4.002e^-5	0.78	SYNONYMOUS_CODING CG1632 DOWNSTREAM Corp	TF binding site mE1_TFBS_chinmo
2R	8873309	2R_8873309_SNP [dm3] 2R_12985804_SNP [dm6]	C	A	4.172e^-5	0.78	EXON CR44339	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_tll BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	21341152	3R_21341152_SNP [dm3] 3R_25515430_SNP [dm6]	A	T	4.189e^-5	0.78	UPSTREAM msi INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	2510953	3L_2510953_SNP [dm3] 3L_2510953_SNP [dm6]	T	G	4.238e^-5	0.78	INTRON Spn
2R	18704014	2R_18704014_SNP [dm3] 2R_22816509_SNP [dm6]	C	G	4.244e^-5	0.78	UTR_5_PRIME CG30271 UPSTREAM CG30271 DOWNSTREAM stl
3L	6652635	3L_6652635_SNP [dm3] 3L_6659535_SNP [dm6]	G	A	4.277e^-5	0.78	INTERGENIC
2L	2738238	2L_2738238_SNP [dm3] 2L_2738238_SNP [dm6]	G	C	4.295e^-5	0.78	SYNONYMOUS_CODING CG31689 DOWNSTREAM mir-4914	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	2738440	2L_2738440_SNP [dm3] 2L_2738440_SNP [dm6]	C	T	4.332e^-5	0.78	SPLICE_SITE_REGION CG31689 DOWNSTREAM mir-4914 INTRON CG31689	TF binding site mE1_TFBS_sens
2L	2738443	2L_2738443_SNP [dm3] 2L_2738443_SNP [dm6]	C	T	4.332e^-5	0.78	SPLICE_SITE_REGION CG31689 DOWNSTREAM mir-4914 INTRON CG31689

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

mn_Weight_LowDiet phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results