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=1.544e^-6)
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

Covariate	p-value	Significance
In_2L_t	0.01282
In_3R_K	7.446e-07

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	11.7412	0.0028
In_3R_K	16.5098	0.0003

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2034 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	12951597	2L_12951597_SNP [dm3] 2L_12951597_SNP [dm6]	C	A	8.813e^-7	0.734	INTERGENIC
2R	8092915	2R_8092915_SNP [dm3] 2R_12205410_SNP [dm6]	C	G	1.542e^-6	0.734	UPSTREAM CR45276 INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	9179925	X_9179925_SNP [dm3] X_9285892_SNP [dm6]	A	C	1.602e^-6	0.734	UTR_5_PRIME lz
3R	5640267	3R_5640267_SNP [dm3] 3R_9814545_SNP [dm6]	G	C	2.004e^-6	0.734	NON_SYNONYMOUS_CODING eloF UPSTREAM CR44035 DOWNSTREAM CG8534	TF binding site mE1_TFBS_sens
2R	8092581	2R_8092581_SNP [dm3] 2R_12205076_SNP [dm6]	C	T	2.163e^-6	0.734	INTERGENIC
2R	8109725	2R_8109725_SNP [dm3] 2R_12222220_SNP [dm6]	G	C	2.818e^-6	0.734	INTERGENIC
3L	5673312	3L_5673312_SNP [dm3] 3L_5680212_SNP [dm6]	G	A	3.401e^-6	0.734	INTRON sif
2L	12951599	2L_12951599_SNP [dm3] 2L_12951599_SNP [dm6]	A	G	3.508e^-6	0.734	INTERGENIC
3L	5673294	3L_5673294_SNP [dm3] 3L_5680194_SNP [dm6]	G	A	3.898e^-6	0.734	INTRON sif
3L	5673273	3L_5673273_SNP [dm3] 3L_5680173_SNP [dm6]	G	T	4.803e^-6	0.734	INTRON sif
3R	14723973	3R_14723973_SNP [dm3] 3R_18898251_SNP [dm6]	G	A	4.863e^-6	0.734	UTR_5_PRIME CG14297
3R	5640310	3R_5640310_SNP [dm3] 3R_9814588_SNP [dm6]	C	A	5.101e^-6	0.734	SYNONYMOUS_CODING eloF UPSTREAM CR44035 DOWNSTREAM CG8534
2R	8092572	2R_8092572_SNP [dm3] 2R_12205067_SNP [dm6]	C	T	5.405e^-6	0.734	INTERGENIC
2R	8383213	2R_8383213_SNP [dm3] 2R_12495708_SNP [dm6]	A	T	5.478e^-6	0.734	UTR_5_PRIME s-cup INTRON fdl
3L	16975630	3L_16975630_SNP [dm3] 3L_16982530_SNP [dm6]	T	A	6.117e^-6	0.765	NON_SYNONYMOUS_CODING Exn	TF binding site mE1_TFBS_cad
3R	3801353	3R_3801353_SNP [dm3] 3R_7975631_SNP [dm6]	T	C	6.985e^-6	0.787	SYNONYMOUS_CODING CD98hc	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	18286355	3R_18286355_SNP [dm3] 3R_22460633_SNP [dm6]	T	G	8.609e^-6	0.787	UTR_3_PRIME CG34376 DOWNSTREAM Rpn7
3R	26914130	3R_26914130_SNP [dm3] 3R_31088408_SNP [dm6]	A	C	9.206e^-6	0.787	INTERGENIC
X	8736742	X_8736742_SNP [dm3] X_8842709_SNP [dm6]	A	T	9.474e^-6	0.787	INTRON CG12075
3R	14670959	3R_14670959_SNP [dm3] 3R_18845237_SNP [dm6]	G	T	9.634e^-6	0.787	INTRON CG18208
3L	16975611	3L_16975611_SNP [dm3] 3L_16982511_SNP [dm6]	G	C	1.008e^-5	0.787	NON_SYNONYMOUS_CODING Exn	TF binding site mE1_TFBS_cad
2R	19387091	2R_19387091_SNP [dm3] 2R_23499568_SNP [dm6]	A	G	1.088e^-5	0.787	UPSTREAM CG13558 INTERGENIC	TF binding site BDTNP1_TFBS_sna
2R	8106248	2R_8106248_INS [dm3] 2R_12218743_INS [dm6]	G	GATG	1.145e^-5	0.787	INTERGENIC
2R	18245408	2R_18245408_SNP [dm3] 2R_22357903_SNP [dm6]	A	G	1.155e^-5	0.787	INTRON Liprin-gamma	transposable element FlyBase
2L	11930160	2L_11930160_SNP [dm3] 2L_11930160_SNP [dm6]	G	A	1.171e^-5	0.787	INTERGENIC
3R	23499267	3R_23499267_SNP [dm3] 3R_27673545_SNP [dm6]	C	A	1.252e^-5	0.787	SYNONYMOUS_CODING unc80	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	8111200	3R_8111200_SNP [dm3] 3R_12285478_SNP [dm6]	T	A	1.330e^-5	0.787	INTRON svp
3L	16972293	3L_16972293_SNP [dm3] 3L_16979193_SNP [dm6]	G	A	1.502e^-5	0.787	INTRON Exn
3L	12184966	3L_12184966_SNP [dm3] 3L_12191866_SNP [dm6]	G	T	1.530e^-5	0.787	NON_SYNONYMOUS_CODING Est-P DOWNSTREAM thoc6
2R	20263325	2R_20263325_SNP [dm3] 2R_24375802_SNP [dm6]	T	C	1.597e^-5	0.787	INTRON bs	TF binding site mE1_TFBS_chinmo
3L	16972296	3L_16972296_SNP [dm3] 3L_16979196_SNP [dm6]	A	T	1.630e^-5	0.787	INTRON Exn
2R	19664071	2R_19664071_SNP [dm3] 2R_23776548_SNP [dm6]	T	A	1.668e^-5	0.787	INTRON CG9850
X	5787789	X_5787789_SNP [dm3] X_5893756_SNP [dm6]	C	T	1.713e^-5	0.787	INTRON CR45668	TF binding site mE1_TFBS_zfh1
2R	8109757	2R_8109757_SNP [dm3] 2R_12222252_SNP [dm6]	A	C	1.790e^-5	0.787	INTERGENIC
2L	1503746	2L_1503746_SNP [dm3] 2L_1503746_SNP [dm6]	G	A	1.832e^-5	0.787	UPSTREAM CG7420 EXON CR44064	TF binding site BDTNP1_TFBS_dl
3L	3020274	3L_3020274_SNP [dm3] 3L_3020274_SNP [dm6]	G	T	1.923e^-5	0.787	INTERGENIC
2R	19666630	2R_19666630_SNP [dm3] 2R_23779107_SNP [dm6]	G	T	1.931e^-5	0.787	NON_SYNONYMOUS_CODING CG9850
2R	19665804	2R_19665804_SNP [dm3] 2R_23778281_SNP [dm6]	G	A	2.066e^-5	0.787	INTRON CG9850
2L	1103147	2L_1103147_SNP [dm3] 2L_1103147_SNP [dm6]	C	A	2.093e^-5	0.787	UPSTREAM CG4629 DOWNSTREAM mtRNApol INTERGENIC
3L	455234	3L_455234_SNP [dm3] 3L_455234_SNP [dm6]	C	G	2.112e^-5	0.787	INTRON klar
2R	19661352	2R_19661352_INS [dm3] 2R_23773829_INS [dm6]	T	TGCT	2.113e^-5	0.787	INTRON CG9850
3R	25136442	3R_25136442_SNP [dm3] 3R_29310720_SNP [dm6]	A	G	2.129e^-5	0.787	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	12185514	3L_12185514_SNP [dm3] 3L_12192414_SNP [dm6]	G	T	2.176e^-5	0.787	NON_SYNONYMOUS_CODING Est-P UTR_3_PRIME thoc6 DOWNSTREAM thoc6
2R	8112845	2R_8112845_SNP [dm3] 2R_12225340_SNP [dm6]	T	C	2.190e^-5	0.787	INTRON CG8854
2R	19664210	2R_19664210_SNP [dm3] 2R_23776687_SNP [dm6]	A	G	2.285e^-5	0.787	INTRON CG9850
3L	16972299	3L_16972299_SNP [dm3] 3L_16979199_SNP [dm6]	G	C	2.313e^-5	0.787	INTRON Exn
2R	11735897	2R_11735897_SNP [dm3] 2R_15848392_SNP [dm6]	T	A	2.321e^-5	0.787	UPSTREAM tun INTRON tun	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_bab1
X	13606673	X_13606673_SNP [dm3] X_13712640_SNP [dm6]	G	T	2.362e^-5	0.787	SYNONYMOUS_CODING NnaD INTRON CG9940
2R	11735901	2R_11735901_SNP [dm3] 2R_15848396_SNP [dm6]	T	C	2.424e^-5	0.787	UPSTREAM tun INTRON tun	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_bab1
X	6439783	X_6439783_SNP [dm3] X_6545750_SNP [dm6]	G	T	2.448e^-5	0.787	UPSTREAM CG34417 INTRON CG34417	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	8112797	2R_8112797_SNP [dm3] 2R_12225292_SNP [dm6]	T	A	2.478e^-5	0.787	INTRON CG8854
2R	20263307	2R_20263307_SNP [dm3] 2R_24375784_SNP [dm6]	C	T	2.485e^-5	0.787	INTRON bs	TF binding site mE1_TFBS_chinmo
2R	20263344	2R_20263344_SNP [dm3] 2R_24375821_SNP [dm6]	C	A	2.485e^-5	0.787	INTRON bs	TF binding site mE1_TFBS_chinmo
2R	8109912	2R_8109912_SNP [dm3] 2R_12222407_SNP [dm6]	C	A	2.559e^-5	0.787	INTERGENIC
3L	11002847	3L_11002847_SNP [dm3] 3L_11009747_SNP [dm6]	T	C	2.626e^-5	0.787	UPSTREAM klu INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
2R	11735874	2R_11735874_SNP [dm3] 2R_15848369_SNP [dm6]	C	A	2.644e^-5	0.787	UPSTREAM tun INTRON tun	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_bab1
X	13606664	X_13606664_SNP [dm3] X_13712631_SNP [dm6]	G	T	2.652e^-5	0.787	SPLICE_SITE_REGION NnaD SYNONYMOUS_CODING NnaD INTRON CG9940
3L	4168404	3L_4168404_SNP [dm3] 3L_4168404_SNP [dm6]	C	A	2.656e^-5	0.787	UPSTREAM mas EXON CR44529	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3L	4168407	3L_4168407_SNP [dm3] 3L_4168407_SNP [dm6]	A	G	2.656e^-5	0.787	UPSTREAM mas EXON CR44529	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2R	8092783	2R_8092783_SNP [dm3] 2R_12205278_SNP [dm6]	G	T	2.660e^-5	0.787	UPSTREAM CR45276 INTERGENIC
2R	8112843	2R_8112843_SNP [dm3] 2R_12225338_SNP [dm6]	T	C	2.661e^-5	0.787	INTRON CG8854
2R	20263207	2R_20263207_SNP [dm3] 2R_24375684_SNP [dm6]	C	A	2.678e^-5	0.787	SYNONYMOUS_CODING bs	TF binding site mE1_TFBS_chinmo
3R	25655818	3R_25655818_SNP [dm3] 3R_29830096_SNP [dm6]	C	G	2.689e^-5	0.787	INTRON Atg16	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	7766736	3R_7766736_SNP [dm3] 3R_11941014_SNP [dm6]	A	C	2.770e^-5	0.787	INTRON Cad87A
2R	8135220	2R_8135220_SNP [dm3] 2R_12247715_SNP [dm6]	T	G	2.805e^-5	0.787	UPSTREAM CR44315 INTERGENIC	transposable element FlyBase
X	6439781	X_6439781_SNP [dm3] X_6545748_SNP [dm6]	G	C	2.847e^-5	0.787	UPSTREAM CG34417 INTRON CG34417	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	16260408	2L_16260408_SNP [dm3] 2L_16260408_SNP [dm6]	G	A	2.865e^-5	0.787	SYNONYMOUS_CODING twe DOWNSTREAM EndoGI	TF binding site mE1_TFBS_cad
2R	8132014	2R_8132014_SNP [dm3] 2R_12244509_SNP [dm6]	C	T	2.918e^-5	0.787	NON_SYNONYMOUS_CODING CG43244
3L	11042828	3L_11042828_SNP [dm3] 3L_11049728_SNP [dm6]	C	T	2.922e^-5	0.787	UPSTREAM CG43693 & 1 other INTRON CG43693
3L	12184935	3L_12184935_SNP [dm3] 3L_12191835_SNP [dm6]	T	A	2.942e^-5	0.787	NON_SYNONYMOUS_CODING Est-P DOWNSTREAM thoc6
3L	5707278	3L_5707278_SNP [dm3] 3L_5714178_SNP [dm6]	C	G	2.989e^-5	0.787	DOWNSTREAM CG44521 INTRON sif
2R	18204852	2R_18204852_DEL [dm3] 2R_22317347_DEL [dm6]	TT	T	3.091e^-5	0.787	UPSTREAM Gp150 DOWNSTREAM CR44758 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	12185525	3L_12185525_SNP [dm3] 3L_12192425_SNP [dm6]	C	T	3.105e^-5	0.787	SPLICE_SITE_ACCEPTOR thoc6 SYNONYMOUS_CODING Est-P DOWNSTREAM thoc6 INTRON thoc6
2R	8135248	2R_8135248_SNP [dm3] 2R_12247743_SNP [dm6]	G	C	3.170e^-5	0.787	UPSTREAM CR44315 INTERGENIC	transposable element FlyBase
2R	8119561	2R_8119561_SNP [dm3] 2R_12232056_SNP [dm6]	C	T	3.245e^-5	0.787	INTERGENIC
3L	12185838	3L_12185838_SNP [dm3] 3L_12192738_SNP [dm6]	G	A	3.255e^-5	0.787	SYNONYMOUS_CODING thoc6 DOWNSTREAM Est-P
3L	5707266	3L_5707266_SNP [dm3] 3L_5714166_SNP [dm6]	T	G	3.315e^-5	0.787	DOWNSTREAM CG44521 INTRON sif
2R	8113408	2R_8113408_SNP [dm3] 2R_12225903_SNP [dm6]	G	T	3.370e^-5	0.787	SYNONYMOUS_CODING CG8854	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	20263303	2R_20263303_SNP [dm3] 2R_24375780_SNP [dm6]	A	G	3.375e^-5	0.787	INTRON bs	TF binding site mE1_TFBS_chinmo
3R	7755363	3R_7755363_SNP [dm3] 3R_11929641_SNP [dm6]	A	T	3.397e^-5	0.787	INTRON Cad87A
2R	19669970	2R_19669970_SNP [dm3] 2R_23782447_SNP [dm6]	T	C	3.457e^-5	0.787	INTRON CG9850	TF binding site mE1_TFBS_chinmo
3L	6129617	3L_6129617_SNP [dm3] 3L_6136517_SNP [dm6]	C	T	3.463e^-5	0.787	NON_SYNONYMOUS_CODING Lcp65Af
3L	12185769	3L_12185769_SNP [dm3] 3L_12192669_SNP [dm6]	A	T	3.531e^-5	0.787	NON_SYNONYMOUS_CODING thoc6 DOWNSTREAM Est-P
3R	9721237	3R_9721237_SNP [dm3] 3R_13895515_SNP [dm6]	T	A	3.559e^-5	0.787	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
X	17654512	X_17654512_SNP [dm3] X_17760479_SNP [dm6]	C	T	3.710e^-5	0.787	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	18982358	3R_18982358_SNP [dm3] 3R_23156636_SNP [dm6]	T	A	3.724e^-5	0.787	INTRON unk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
X	17654508	X_17654508_SNP [dm3] X_17760475_SNP [dm6]	G	T	3.798e^-5	0.787	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	16972288	3L_16972288_SNP [dm3] 3L_16979188_SNP [dm6]	T	G	3.928e^-5	0.787	INTRON Exn
2R	8116777	2R_8116777_SNP [dm3] 2R_12229272_SNP [dm6]	C	A	3.937e^-5	0.787	UTR_5_PRIME CG8854
3L	11002850	3L_11002850_SNP [dm3] 3L_11009750_SNP [dm6]	C	T	3.966e^-5	0.787	UPSTREAM klu INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
3R	18982520	3R_18982520_SNP [dm3] 3R_23156798_SNP [dm6]	A	G	4.008e^-5	0.787	INTRON unk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_zfh1
2L	4681170	2L_4681170_SNP [dm3] 2L_4681170_SNP [dm6]	T	C	4.058e^-5	0.787	INTERGENIC
2R	8077706	2R_8077706_SNP [dm3] 2R_12190201_SNP [dm6]	G	T	4.083e^-5	0.787	SYNONYMOUS_CODING Cyp6g2 UPSTREAM Cyp6t3	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	12738525	3R_12738525_DEL [dm3] 3R_16912803_DEL [dm6]	AA	A	4.172e^-5	0.787	INTRON iab-8	TF binding site BDTNP1_TFBS_dl
3L	16972320	3L_16972320_SNP [dm3] 3L_16979220_SNP [dm6]	A	G	4.174e^-5	0.787	INTRON Exn
2R	8114368	2R_8114368_SNP [dm3] 2R_12226863_SNP [dm6]	T	C	4.234e^-5	0.787	UPSTREAM CG8854 INTRON CG8854	TF binding site mE1_TFBS_inv
X	3958470	X_3958470_SNP [dm3] X_4064437_SNP [dm6]	G	T	4.241e^-5	0.787	INTERGENIC
2R	8112670	2R_8112670_SNP [dm3] 2R_12225165_SNP [dm6]	C	T	4.265e^-5	0.787	SYNONYMOUS_CODING CG8854	TF binding site mE1_TFBS_chinmo
2L	2304603	2L_2304603_SNP [dm3] 2L_2304603_SNP [dm6]	C	T	4.282e^-5	0.787	INTERGENIC
3L	20386809	3L_20386809_SNP [dm3] 3L_20393709_SNP [dm6]	C	G	4.285e^-5	0.787	UPSTREAM CG33969 INTERGENIC	TF binding site mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

Missing results

By genomic position
Variant impact
Gene name

Cuticul_5_9_C29_1_2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results