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=9.983e^-16)
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_3R_K	2.089e-13

Kruskal-Wallis test

Covariate	χ²	p-value	Significance

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2096 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	15013402	2L_15013402_SNP [dm3] 2L_15013402_SNP [dm6]	A	T	7.486e^-8	0.14	UPSTREAM CR43856 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	13541077	2L_13541077_SNP [dm3] 2L_13541077_SNP [dm6]	T	C	4.180e^-7	0.392	DOWNSTREAM CG9263 INTRON B4 & 1 other	TF binding site mE1_TFBS_HSA
2L	13541073	2L_13541073_SNP [dm3] 2L_13541073_SNP [dm6]	A	T	9.659e^-7	0.604	DOWNSTREAM CG9263 INTRON B4 & 1 other	TF binding site mE1_TFBS_HSA
3R	12509672	3R_12509672_SNP [dm3] 3R_16683950_SNP [dm6]	T	C	1.565e^-6	0.661	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
2R	7986830	2R_7986830_SNP [dm3] 2R_12099325_SNP [dm6]	A	G	2.146e^-6	0.661	INTRON jeb	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	13647627	3R_13647627_SNP [dm3] 3R_17821905_SNP [dm6]	T	A	3.211e^-6	0.661	UTR_5_PRIME tinc INTRON tinc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2L	15881899	2L_15881899_SNP [dm3] 2L_15881899_SNP [dm6]	T	A	3.805e^-6	0.661	DOWNSTREAM CG44475 INTERGENIC	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_HSA
3R	12502353	3R_12502353_SNP [dm3] 3R_16676631_SNP [dm6]	C	T	3.911e^-6	0.661	INTRON Ubx	TF binding site mE1_TFBS_cad
2L	15881902	2L_15881902_SNP [dm3] 2L_15881902_SNP [dm6]	A	G	4.849e^-6	0.661	DOWNSTREAM CG44475 INTERGENIC	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_HSA
2L	13541089	2L_13541089_SNP [dm3] 2L_13541089_SNP [dm6]	C	T	5.021e^-6	0.661	DOWNSTREAM CG9263 INTRON B4 & 1 other	TF binding site mE1_TFBS_HSA
2L	4712572	2L_4712572_SNP [dm3] 2L_4712572_SNP [dm6]	A	G	5.265e^-6	0.661	INTRON CG34351
2L	15883347	2L_15883347_SNP [dm3] 2L_15883347_SNP [dm6]	T	C	5.885e^-6	0.661	UPSTREAM CG44475 INTERGENIC
3R	9053286	3R_9053286_SNP [dm3] 3R_13227564_SNP [dm6]	A	G	6.180e^-6	0.661	UTR_3_PRIME Ace DOWNSTREAM Ace INTRON Ace
2R	14536543	2R_14536543_SNP [dm3] 2R_18649038_SNP [dm6]	A	G	6.202e^-6	0.661	INTRON SP2637
3R	15458329	3R_15458329_SNP [dm3] 3R_19632607_SNP [dm6]	C	T	6.681e^-6	0.661	UTR_5_PRIME CG6231 DOWNSTREAM subdued	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	19609269	3R_19609269_SNP [dm3] 3R_23783547_SNP [dm6]	G	A	7.155e^-6	0.661	INTRON mbc	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
3R	12509571	3R_12509571_SNP [dm3] 3R_16683849_SNP [dm6]	C	A	7.525e^-6	0.661	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
3R	12859507	3R_12859507_SNP [dm3] 3R_17033785_SNP [dm6]	G	A	8.335e^-6	0.661	UTR_3_PRIME CG4009 DOWNSTREAM CG31268
2L	13541115	2L_13541115_SNP [dm3] 2L_13541115_SNP [dm6]	T	A	8.493e^-6	0.661	DOWNSTREAM CG9263 INTRON B4 & 1 other	TF binding site mE1_TFBS_HSA
3R	19208501	3R_19208501_SNP [dm3] 3R_23382779_SNP [dm6]	T	C	8.861e^-6	0.661	UTR_5_PRIME CG4393 INTRON CG4393
3R	12508877	3R_12508877_SNP [dm3] 3R_16683155_SNP [dm6]	A	C	9.020e^-6	0.661	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	14860809	3R_14860809_SNP [dm3] 3R_19035087_SNP [dm6]	A	C	9.518e^-6	0.661	INTRON CG6026
2L	12924149	2L_12924149_SNP [dm3] 2L_12924149_SNP [dm6]	A	G	9.897e^-6	0.661	INTRON ACXA	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2R	12969093	2R_12969093_DEL [dm3] 2R_17081588_DEL [dm6]	TT	T	1.035e^-5	0.661	UTR_5_PRIME CG30460
3R	14860908	3R_14860908_SNP [dm3] 3R_19035186_SNP [dm6]	T	G	1.089e^-5	0.661	INTRON CG6026
2R	13789677	2R_13789677_SNP [dm3] 2R_17902172_SNP [dm6]	G	A	1.106e^-5	0.661	INTRON Elk
2L	2604839	2L_2604839_SNP [dm3] 2L_2604839_SNP [dm6]	G	C	1.121e^-5	0.661	INTERGENIC
2L	2693939	2L_2693939_SNP [dm3] 2L_2693939_SNP [dm6]	T	C	1.123e^-5	0.661	INTRON CG31690
2L	15336280	2L_15336280_INS [dm3] 2L_15336280_INS [dm6]	T	TGTTA	1.146e^-5	0.661	DOWNSTREAM esg INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	12891472	3R_12891472_SNP [dm3] 3R_17065750_SNP [dm6]	T	A	1.150e^-5	0.661	INTRON Dad	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Trl
2L	5630919	2L_5630919_SNP [dm3] 2L_5630919_SNP [dm6]	G	A	1.159e^-5	0.661	DOWNSTREAM CR44822 INTRON CG31646	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3R	12501869	3R_12501869_SNP [dm3] 3R_16676147_SNP [dm6]	G	T	1.171e^-5	0.661	INTRON Ubx	TF binding site mE1_TFBS_cad
2L	15949393	2L_15949393_DEL [dm3] 2L_15949393_DEL [dm6]	ATAGTTTCA	A	1.198e^-5	0.661	INTRON beat-Ib
2L	8071858	2L_8071858_SNP [dm3] 2L_8071858_SNP [dm6]	C	T	1.233e^-5	0.661	UTR_3_PRIME MED20 UPSTREAM poe	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	9523155	3L_9523155_SNP [dm3] 3L_9530055_SNP [dm6]	A	G	1.253e^-5	0.661	SYNONYMOUS_CODING Or67a
X	20320580	X_20320580_SNP [dm3] X_20449553_SNP [dm6]	C	A	1.294e^-5	0.661	UTR_5_PRIME CG32506
3R	26251010	3R_26251010_SNP [dm3] 3R_30425288_SNP [dm6]	C	T	1.303e^-5	0.661	UPSTREAM CG15536 DOWNSTREAM CG2218 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	3856843	2L_3856843_SNP [dm3] 2L_3856843_SNP [dm6]	G	A	1.340e^-5	0.661	EXON CR45450	TF binding site mE1_TFBS_cnc mE1_TFBS_sens
2R	20184952	2R_20184952_SNP [dm3] 2R_24297429_SNP [dm6]	C	T	1.475e^-5	0.702	INTRON CG3394	TF binding site mE1_TFBS_chinmo
2L	3735421	2L_3735421_INS [dm3] 2L_3735421_INS [dm6]	T	TT	1.498e^-5	0.702	INTRON CG10019
2L	12928584	2L_12928584_SNP [dm3] 2L_12928584_SNP [dm6]	T	A	1.620e^-5	0.721	INTRON ACXE
2R	10607384	2R_10607384_SNP [dm3] 2R_14719879_SNP [dm6]	G	A	1.692e^-5	0.721	INTERGENIC
2L	2338755	2L_2338755_SNP [dm3] 2L_2338755_SNP [dm6]	T	C	1.750e^-5	0.721	INTRON CG9967 & 1 other
3L	4436839	3L_4436839_SNP [dm3] 3L_4436839_SNP [dm6]	T	C	1.775e^-5	0.721	UTR_5_PRIME CG15021 DOWNSTREAM nAChRbeta1	TF binding site mE1_TFBS_cad
2R	6357172	2R_6357172_SNP [dm3] 2R_10469667_SNP [dm6]	C	G	1.834e^-5	0.721	UTR_3_PRIME whd DOWNSTREAM CG11777
2R	20184413	2R_20184413_SNP [dm3] 2R_24296890_SNP [dm6]	G	T	1.853e^-5	0.721	NON_SYNONYMOUS_CODING CG3394	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	15107994	2R_15107994_SNP [dm3] 2R_19220489_SNP [dm6]	T	G	1.860e^-5	0.721	INTRON hppy
3L	16018928	3L_16018928_SNP [dm3] 3L_16025828_SNP [dm6]	T	G	1.887e^-5	0.721	INTRON Notum	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
3R	12896174	3R_12896174_SNP [dm3] 3R_17070452_SNP [dm6]	A	G	1.908e^-5	0.721	DOWNSTREAM Ns1 & 1 other INTERGENIC
2R	15107963	2R_15107963_SNP [dm3] 2R_19220458_SNP [dm6]	A	G	1.940e^-5	0.721	INTRON hppy
3R	14350273	3R_14350273_SNP [dm3] 3R_18524551_SNP [dm6]	C	G	1.971e^-5	0.721	INTRON fru
2R	15107996	2R_15107996_SNP [dm3] 2R_19220491_SNP [dm6]	A	G	1.998e^-5	0.721	INTRON hppy
3L	12716666	3L_12716666_SNP [dm3] 3L_12723566_SNP [dm6]	A	C	2.131e^-5	0.748	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12633680	3R_12633680_SNP [dm3] 3R_16807958_SNP [dm6]	G	C	2.252e^-5	0.748	UTR_3_PRIME abd-A
3L	12716676	3L_12716676_SNP [dm3] 3L_12723576_SNP [dm6]	G	A	2.262e^-5	0.748	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	15883377	2L_15883377_SNP [dm3] 2L_15883377_SNP [dm6]	A	C	2.273e^-5	0.748	UPSTREAM CG44475 INTERGENIC
3L	12717223	3L_12717223_SNP [dm3] 3L_12724123_SNP [dm6]	T	G	2.288e^-5	0.748	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	17614699	2L_17614699_DEL [dm3] 2L_17614699_DEL [dm6]	TTCGAATGTTTTGCCTTTTT...	T	2.333e^-5	0.748	INTERGENIC
2L	2914785	2L_2914785_SNP [dm3] 2L_2914785_SNP [dm6]	C	T	2.471e^-5	0.748	INTRON lilli
2L	2331592	2L_2331592_SNP [dm3] 2L_2331592_SNP [dm6]	C	T	2.482e^-5	0.748	INTRON CG9967 & 1 other
2L	7378036	2L_7378036_SNP [dm3] 2L_7378036_SNP [dm6]	A	G	2.509e^-5	0.748	DOWNSTREAM Wnt10 INTRON ninaC
3L	12878190	3L_12878190_SNP [dm3] 3L_12885090_SNP [dm6]	G	T	2.510e^-5	0.748	SYNONYMOUS_CODING CG14120	TF binding site mE1_TFBS_inv
3R	13364021	3R_13364021_SNP [dm3] 3R_17538299_SNP [dm6]	A	G	2.512e^-5	0.748	NON_SYNONYMOUS_CODING l_3_07882	TF binding site mE1_TFBS_sens
2L	2331572	2L_2331572_SNP [dm3] 2L_2331572_SNP [dm6]	C	A	2.618e^-5	0.753	INTRON CG9967 & 1 other
3R	13170756	3R_13170756_SNP [dm3] 3R_17345034_SNP [dm6]	G	A	2.624e^-5	0.753	INTRON beat-IIa
2L	9491186	2L_9491186_INS [dm3] 2L_9491186_INS [dm6]	A	TTT	2.651e^-5	0.753	UTR_3_PRIME Gdi DOWNSTREAM Gdi
2L	751683	2L_751683_SNP [dm3] 2L_751683_SNP [dm6]	G	C	2.753e^-5	0.771	INTRON GABA-B-R3
2L	15883414	2L_15883414_SNP [dm3] 2L_15883414_SNP [dm6]	A	T	2.827e^-5	0.78	UPSTREAM CG44475 INTERGENIC
3R	12512612	3R_12512612_SNP [dm3] 3R_16686890_SNP [dm6]	A	T	2.951e^-5	0.797	INTRON Ubx	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	2338844	2L_2338844_SNP [dm3] 2L_2338844_SNP [dm6]	C	A	2.982e^-5	0.797	SYNONYMOUS_CODING eys INTRON CG9967
3L	3598641	3L_3598641_SNP [dm3] 3L_3598641_SNP [dm6]	T	G	3.075e^-5	0.797	INTRON Eip63E	TF binding site mE1_TFBS_cad
3R	13170887	3R_13170887_DEL [dm3] 3R_17345165_DEL [dm6]	CTAGAGGATAA...	C	3.084e^-5	0.797	INTRON beat-IIa
3R	26247669	3R_26247669_SNP [dm3] 3R_30421947_SNP [dm6]	G	A	3.104e^-5	0.797	SYNONYMOUS_CODING CG2217 UTR_5_PRIME CG42740	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	8363041	2L_8363041_INS [dm3] 2L_8363041_INS [dm6]	T	TAT	3.206e^-5	0.797	UPSTREAM CG7627 DOWNSTREAM RpS13 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17552816	2R_17552816_SNP [dm3] 2R_21665311_SNP [dm6]	A	G	3.230e^-5	0.797	SYNONYMOUS_CODING CG42363 UTR_3_PRIME CG42362 UPSTREAM CG42364
2L	2338272	2L_2338272_SNP [dm3] 2L_2338272_SNP [dm6]	C	T	3.263e^-5	0.797	INTRON CG9967 & 1 other
3R	6692156	3R_6692156_SNP [dm3] 3R_10866434_SNP [dm6]	A	G	3.326e^-5	0.797	INTRON SelR
3R	13170746	3R_13170746_INS [dm3] 3R_17345024_INS [dm6]	G	GG	3.434e^-5	0.797	INTRON beat-IIa
3L	18745736	3L_18745736_SNP [dm3] 3L_18752636_SNP [dm6]	T	C	3.461e^-5	0.797	UTR_3_PRIME ftz-f1
X	18216351	X_18216351_SNP [dm3] X_18322318_SNP [dm6]	C	A	3.461e^-5	0.797	DOWNSTREAM CG6123 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	25600401	3R_25600401_SNP [dm3] 3R_29774679_SNP [dm6]	C	T	3.463e^-5	0.797	INTRON kay	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	15458311	3R_15458311_SNP [dm3] 3R_19632589_SNP [dm6]	C	A	3.649e^-5	0.797	UTR_5_PRIME CG6231 DOWNSTREAM subdued	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	17240671	3R_17240671_SNP [dm3] 3R_21414949_SNP [dm6]	T	A	3.680e^-5	0.797	INTRON lbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA
2L	14675930	2L_14675930_SNP [dm3] 2L_14675930_SNP [dm6]	C	T	3.765e^-5	0.797	INTRON osp
2L	2337644	2L_2337644_SNP [dm3] 2L_2337644_SNP [dm6]	C	G	3.868e^-5	0.797	INTRON CG9967 & 1 other
2L	14675935	2L_14675935_SNP [dm3] 2L_14675935_SNP [dm6]	T	C	3.878e^-5	0.797	INTRON osp
3R	18814727	3R_18814727_SNP [dm3] 3R_22989005_SNP [dm6]	G	A	4.039e^-5	0.797	UPSTREAM Or94b DOWNSTREAM Or94a INTRON Nha2
2R	1137803	2R_1137803_SNP [dm3] 2R_5250298_SNP [dm6]	T	C	4.140e^-5	0.797	INTRON Nipped-A
3R	9163195	3R_9163195_SNP [dm3] 3R_13337473_SNP [dm6]	G	C	4.199e^-5	0.797	UPSTREAM PK2-R1 INTERGENIC
2R	15174933	2R_15174933_SNP [dm3] 2R_19287428_SNP [dm6]	A	T	4.239e^-5	0.797	UPSTREAM CG10474 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12872247	3R_12872247_SNP [dm3] 3R_17046525_SNP [dm6]	T	A	4.245e^-5	0.797	INTRON Patr-1
2L	12928644	2L_12928644_SNP [dm3] 2L_12928644_SNP [dm6]	G	A	4.279e^-5	0.797	SYNONYMOUS_CODING ACXE
X	10873491	X_10873491_DEL [dm3] X_10979458_DEL [dm6]	CAAAAATGGA	C	4.291e^-5	0.797	INTRON CG42339
2L	6982358	2L_6982358_SNP [dm3] 2L_6982358_SNP [dm6]	G	A	4.296e^-5	0.797	SYNONYMOUS_CODING uif	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14928006	2R_14928006_DEL [dm3] 2R_19040501_DEL [dm6]	GG	G	4.330e^-5	0.797	INTERGENIC
2L	15883369	2L_15883369_SNP [dm3] 2L_15883369_SNP [dm6]	T	A	4.417e^-5	0.797	UPSTREAM CG44475 INTERGENIC
3R	13934867	3R_13934867_SNP [dm3] 3R_18109145_SNP [dm6]	G	A	4.524e^-5	0.797	DOWNSTREAM tRNA:CR31242 & 1 other INTRON sr
2L	15914696	2L_15914696_SNP [dm3] 2L_15914696_SNP [dm6]	C	T	4.603e^-5	0.797	INTRON beat-Ib
2L	8275998	2L_8275998_SNP [dm3] 2L_8275998_SNP [dm6]	G	A	4.676e^-5	0.797	INTRON Btk29A	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	14433858	2L_14433858_SNP [dm3] 2L_14433858_SNP [dm6]	A	G	4.695e^-5	0.797	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_3_Me_C25_C26 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results