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=3.025e^-4)
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
wolba	0.01239
In_3R_P	0.02435

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	3.886	0.0487
In_3R_P	8.5755	0.0137

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2017 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
3L	6052264	3L_6052264_SNP [dm3] 3L_6059164_SNP [dm6]	C	A	1.191e^-7	0.097	UPSTREAM CG6592 EXON CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
3L	6051581	3L_6051581_SNP [dm3] 3L_6058481_SNP [dm6]	A	C	1.725e^-7	0.097	UPSTREAM CR45441 INTERGENIC
3L	6052817	3L_6052817_SNP [dm3] 3L_6059717_SNP [dm6]	T	A	1.735e^-7	0.097	UTR_5_PRIME CG6592 DOWNSTREAM CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_chinmo mE1_TFBS_inv
3L	6051448	3L_6051448_SNP [dm3] 3L_6058348_SNP [dm6]	G	A	2.159e^-7	0.097	UPSTREAM CR45441 INTERGENIC
3L	6052786	3L_6052786_SNP [dm3] 3L_6059686_SNP [dm6]	A	G	3.182e^-7	0.097	UTR_5_PRIME CG6592 DOWNSTREAM CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_chinmo mE1_TFBS_inv mE1_TFBS_run
3L	6051559	3L_6051559_SNP [dm3] 3L_6058459_SNP [dm6]	C	T	3.902e^-7	0.097	UPSTREAM CR45441 INTERGENIC
3L	6052787	3L_6052787_SNP [dm3] 3L_6059687_SNP [dm6]	T	A	4.128e^-7	0.097	UTR_5_PRIME CG6592 DOWNSTREAM CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_chinmo mE1_TFBS_inv mE1_TFBS_run
3L	6052223	3L_6052223_DEL [dm3] 3L_6059123_DEL [dm6]	TT	T	4.182e^-7	0.097	UPSTREAM CG6592 EXON CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
2L	20762600	2L_20762600_SNP [dm3] 2L_20762600_SNP [dm6]	A	G	4.927e^-7	0.097	DOWNSTREAM dia INTRON dia	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	6051392	3L_6051392_SNP [dm3] 3L_6058292_SNP [dm6]	T	C	5.260e^-7	0.097	UPSTREAM CR45441 INTERGENIC
3L	6052819	3L_6052819_SNP [dm3] 3L_6059719_SNP [dm6]	A	T	5.706e^-7	0.097	START_GAINED CG6592 UTR_5_PRIME CG6592 DOWNSTREAM CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_chinmo mE1_TFBS_inv
3L	6051357	3L_6051357_SNP [dm3] 3L_6058257_SNP [dm6]	C	T	6.898e^-7	0.108	UPSTREAM CR45441 INTERGENIC
3L	6052241	3L_6052241_SNP [dm3] 3L_6059141_SNP [dm6]	C	T	9.484e^-7	0.137	UPSTREAM CG6592 EXON CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run
2L	9410908	2L_9410908_SNP [dm3] 2L_9410908_SNP [dm6]	C	A	1.041e^-6	0.139	INTRON Shawl
3L	6051362	3L_6051362_SNP [dm3] 3L_6058262_SNP [dm6]	G	A	1.302e^-6	0.163	UPSTREAM CR45441 INTERGENIC
2L	9413340	2L_9413340_SNP [dm3] 2L_9413340_SNP [dm6]	C	T	1.640e^-6	0.192	INTRON Shawl
3R	7186858	3R_7186858_SNP [dm3] 3R_11361136_SNP [dm6]	A	G	2.846e^-6	0.314	INTRON pros	regulatory region REDfly_CRMs TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2L	9409920	2L_9409920_SNP [dm3] 2L_9409920_SNP [dm6]	A	T	3.741e^-6	0.39	INTRON Shawl
2L	9688870	2L_9688870_SNP [dm3] 2L_9688870_SNP [dm6]	C	A	3.991e^-6	0.394	INTRON Pka-C1
3R	21710760	3R_21710760_SNP [dm3] 3R_25885038_SNP [dm6]	G	T	4.805e^-6	0.424	INTRON SppL	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	17575549	2R_17575549_SNP [dm3] 2R_21688044_SNP [dm6]	A	C	4.833e^-6	0.424	UTR_3_PRIME CG30285 UPSTREAM Tbp & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA
X	12114932	X_12114932_DEL [dm3] X_12220899_DEL [dm6]	CC	C	4.971e^-6	0.424	INTRON Ten-a
3L	6051650	3L_6051650_SNP [dm3] 3L_6058550_SNP [dm6]	A	G	5.207e^-6	0.425	UPSTREAM CR45441 INTERGENIC
2L	9408943	2L_9408943_DEL [dm3] 2L_9408943_DEL [dm6]	TT	C	5.864e^-6	0.458	INTRON Shawl
2R	17575554	2R_17575554_SNP [dm3] 2R_21688049_SNP [dm6]	A	G	6.342e^-6	0.459	UTR_3_PRIME CG30285 UPSTREAM Tbp & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA
3L	6052802	3L_6052802_SNP [dm3] 3L_6059702_SNP [dm6]	T	G	6.368e^-6	0.459	UTR_5_PRIME CG6592 DOWNSTREAM CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_chinmo mE1_TFBS_inv mE1_TFBS_run
2R	17575553	2R_17575553_SNP [dm3] 2R_21688048_SNP [dm6]	G	A	7.026e^-6	0.486	UTR_3_PRIME CG30285 UPSTREAM Tbp & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA
2L	9411012	2L_9411012_SNP [dm3] 2L_9411012_SNP [dm6]	A	T	7.425e^-6	0.486	INTRON Shawl
2L	2878619	2L_2878619_SNP [dm3] 2L_2878619_SNP [dm6]	G	A	7.899e^-6	0.486	SYNONYMOUS_CODING CG31950 UPSTREAM betaggt-II & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
X	9188540	X_9188540_SNP [dm3] X_9294507_SNP [dm6]	T	A	8.051e^-6	0.486	INTRON lz	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13915193	2R_13915193_SNP [dm3] 2R_18027688_SNP [dm6]	A	G	8.072e^-6	0.486	INTERGENIC
2L	9411013	2L_9411013_SNP [dm3] 2L_9411013_SNP [dm6]	C	T	8.412e^-6	0.486	INTRON Shawl
2L	9414777	2L_9414777_SNP [dm3] 2L_9414777_SNP [dm6]	G	A	8.813e^-6	0.486	INTRON Shawl
X	8557806	X_8557806_SNP [dm3] X_8663773_SNP [dm6]	A	G	8.862e^-6	0.486	INTERGENIC	TF binding site mE1_TFBS_sbb
2R	9746415	2R_9746415_DEL [dm3] 2R_13858910_DEL [dm6]	TC	T	9.077e^-6	0.486	UPSTREAM Uba3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	4369909	3L_4369909_SNP [dm3] 3L_4369909_SNP [dm6]	T	C	9.842e^-6	0.491	SYNONYMOUS_CODING DopEcR
2R	17575558	2R_17575558_SNP [dm3] 2R_21688053_SNP [dm6]	A	G	9.868e^-6	0.491	UTR_3_PRIME CG30285 UPSTREAM Tbp & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA
3L	6050576	3L_6050576_SNP [dm3] 3L_6057476_SNP [dm6]	T	A	9.943e^-6	0.491	DOWNSTREAM tan INTERGENIC
2L	18916070	2L_18916070_DEL [dm3] 2L_18916070_DEL [dm6]	TCTCCGT	T	1.094e^-5	0.526	DOWNSTREAM ssp3 INTERGENIC
2L	9406873	2L_9406873_SNP [dm3] 2L_9406873_SNP [dm6]	A	T	1.156e^-5	0.542	INTRON Shawl
3L	6050266	3L_6050266_SNP [dm3] 3L_6057166_SNP [dm6]	A	G	1.219e^-5	0.551	DOWNSTREAM tan INTERGENIC
3L	9026764	3L_9026764_SNP [dm3] 3L_9033664_SNP [dm6]	A	G	1.236e^-5	0.551	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3L	6051503	3L_6051503_SNP [dm3] 3L_6058403_SNP [dm6]	C	A	1.316e^-5	0.551	UPSTREAM CR45441 INTERGENIC
3L	9026833	3L_9026833_SNP [dm3] 3L_9033733_SNP [dm6]	A	T	1.318e^-5	0.551	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3L	19035095	3L_19035095_SNP [dm3] 3L_19041995_SNP [dm6]	A	C	1.367e^-5	0.551	INTRON nkd	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
2L	2609851	2L_2609851_SNP [dm3] 2L_2609851_SNP [dm6]	T	C	1.372e^-5	0.551	UPSTREAM CG15395 INTERGENIC
3L	14956462	3L_14956462_SNP [dm3] 3L_14963362_SNP [dm6]	G	C	1.417e^-5	0.551	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	9411529	2L_9411529_SNP [dm3] 2L_9411529_SNP [dm6]	A	T	1.441e^-5	0.551	INTRON Shawl
2L	9406822	2L_9406822_SNP [dm3] 2L_9406822_SNP [dm6]	A	T	1.481e^-5	0.551	INTRON Shawl
2L	9414063	2L_9414063_SNP [dm3] 2L_9414063_SNP [dm6]	T	C	1.498e^-5	0.551	INTRON Shawl
3R	23796935	3R_23796935_SNP [dm3] 3R_27971213_SNP [dm6]	G	T	1.525e^-5	0.551	INTRON betaTub97EF
3R	25670940	3R_25670940_SNP [dm3] 3R_29845218_SNP [dm6]	C	T	1.527e^-5	0.551	INTRON Cad99C
2L	8353388	2L_8353388_SNP [dm3] 2L_8353388_SNP [dm6]	C	A	1.712e^-5	0.598	NON_SYNONYMOUS_CODING Mur29B	TF binding site mE1_TFBS_sens
2L	9408941	2L_9408941_SNP [dm3] 2L_9408941_SNP [dm6]	A	C	1.722e^-5	0.598	INTRON Shawl
3L	6053489	3L_6053489_SNP [dm3] 3L_6060389_SNP [dm6]	T	G	1.787e^-5	0.607	SYNONYMOUS_CODING CG6592 DOWNSTREAM CR45441 & 1 other	TF binding site mE1_TFBS_chinmo mE1_TFBS_inv
3R	26717633	3R_26717633_SNP [dm3] 3R_30891911_SNP [dm6]	C	T	1.812e^-5	0.607	INTERGENIC
2L	3742353	2L_3742353_DEL [dm3] 2L_3742353_DEL [dm6]	AC	A	1.885e^-5	0.62	INTRON CG10019
2L	10115204	2L_10115204_SNP [dm3] 2L_10115204_SNP [dm6]	T	G	1.950e^-5	0.631	INTRON CG44153 & 1 other
3R	25816152	3R_25816152_SNP [dm3] 3R_29990430_SNP [dm6]	T	C	1.994e^-5	0.634	SYNONYMOUS_CODING CG7896 DOWNSTREAM Acph-1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10155111	2L_10155111_SNP [dm3] 2L_10155111_SNP [dm6]	A	G	2.040e^-5	0.638	SYNONYMOUS_CODING CG4839 INTRON CG44153
2R	15383423	2R_15383423_SNP [dm3] 2R_19495918_SNP [dm6]	C	T	2.119e^-5	0.652	SYNONYMOUS_CODING hpo	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	3703134	2L_3703134_SNP [dm3] 2L_3703134_SNP [dm6]	G	A	2.207e^-5	0.668	UPSTREAM CG2816 DOWNSTREAM CG43145 & 2 others INTERGENIC
3L	9900286	3L_9900286_SNP [dm3] 3L_9907186_SNP [dm6]	C	T	2.271e^-5	0.673	UPSTREAM CG34356 INTERGENIC
3R	9635547	3R_9635547_SNP [dm3] 3R_13809825_SNP [dm6]	G	A	2.296e^-5	0.673	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
X	18412846	X_18412846_SNP [dm3] X_18518813_SNP [dm6]	C	T	2.333e^-5	0.673	INTRON Bx & 1 other	TF binding site mE1_TFBS_chinmo
2L	11213150	2L_11213150_SNP [dm3] 2L_11213150_SNP [dm6]	A	T	2.442e^-5	0.689	INTRON ab
X	4495203	X_4495203_INS [dm3] X_4601170_INS [dm6]	A	AAA	2.462e^-5	0.689	INTRON CR32773
2L	9303748	2L_9303748_INS [dm3] 2L_9303748_INS [dm6]	G	GTCGTGGCAATG...	2.528e^-5	0.691	DOWNSTREAM CR42844 INTERGENIC
3R	12295752	3R_12295752_SNP [dm3] 3R_16470030_SNP [dm6]	A	C	2.567e^-5	0.691	UPSTREAM CSN5 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9688836	2L_9688836_SNP [dm3] 2L_9688836_SNP [dm6]	T	G	2.613e^-5	0.691	INTRON Pka-C1
2L	6086077	2L_6086077_SNP [dm3] 2L_6086077_SNP [dm6]	A	T	2.634e^-5	0.691	INTRON Kr-h1	TF binding site mE1_TFBS_inv
3L	3079693	3L_3079693_SNP [dm3] 3L_3079693_SNP [dm6]	G	A	2.715e^-5	0.691	INTRON CG11486
2R	17653000	2R_17653000_SNP [dm3] 2R_21765495_SNP [dm6]	T	C	2.731e^-5	0.691	UTR_5_PRIME CG30395 UPSTREAM CR43984 DOWNSTREAM CG43982
2L	9413355	2L_9413355_SNP [dm3] 2L_9413355_SNP [dm6]	G	A	2.749e^-5	0.691	INTRON Shawl
2L	5514338	2L_5514338_SNP [dm3] 2L_5514338_SNP [dm6]	A	C	2.761e^-5	0.691	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1590090	2L_1590090_SNP [dm3] 2L_1590090_SNP [dm6]	G	A	2.891e^-5	0.714	INTRON haf
3L	6052949	3L_6052949_SNP [dm3] 3L_6059849_SNP [dm6]	T	C	3.004e^-5	0.723	UTR_5_PRIME CG6592 DOWNSTREAM CR45441	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	8543458	2R_8543458_DEL [dm3] 2R_12655953_DEL [dm6]	TT	T	3.021e^-5	0.723	UTR_5_PRIME CG8646 DOWNSTREAM ZnT49B
3L	6110981	3L_6110981_SNP [dm3] 3L_6117881_SNP [dm6]	C	G	3.067e^-5	0.723	INTRON Ets65A
3L	6051898	3L_6051898_SNP [dm3] 3L_6058798_SNP [dm6]	A	G	3.085e^-5	0.723	UPSTREAM CR45441 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_run
2R	17653174	2R_17653174_SNP [dm3] 2R_21765669_SNP [dm6]	A	C	3.143e^-5	0.728	NON_SYNONYMOUS_CODING CG30395 UPSTREAM CR43984 DOWNSTREAM CG43982
2R	10695744	2R_10695744_SNP [dm3] 2R_14808239_SNP [dm6]	T	A	3.268e^-5	0.748	UPSTREAM hui INTERGENIC	regulatory region REDfly_CRMs
2R	17653188	2R_17653188_SNP [dm3] 2R_21765683_SNP [dm6]	T	C	3.556e^-5	0.804	SPLICE_SITE_REGION CG30395 SYNONYMOUS_CODING CG30395 UPSTREAM CR43984 DOWNSTREAM CG43982
2L	19455403	2L_19455403_SNP [dm3] 2L_19455403_SNP [dm6]	C	T	3.654e^-5	0.816	UPSTREAM CG10026 INTRON CG10026
3L	6051493	3L_6051493_SNP [dm3] 3L_6058393_SNP [dm6]	A	T	3.950e^-5	0.845	UPSTREAM CR45441 INTERGENIC
3L	6106839	3L_6106839_DEL [dm3] 3L_6113739_DEL [dm6]	AA	A	4.035e^-5	0.845	INTRON Ets65A
2L	9410128	2L_9410128_SNP [dm3] 2L_9410128_SNP [dm6]	T	C	4.141e^-5	0.845	INTRON Shawl
3L	3079755	3L_3079755_INS [dm3] 3L_3079755_INS [dm6]	G	GTTTGAAGTTGCTTTATTA...	4.143e^-5	0.845	INTRON CG11486
2R	9746412	2R_9746412_SNP [dm3] 2R_13858907_SNP [dm6]	A	C	4.163e^-5	0.845	UPSTREAM Uba3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2L	20767383	2L_20767383_SNP [dm3] 2L_20767383_SNP [dm6]	G	A	4.176e^-5	0.845	UTR_3_PRIME dia DOWNSTREAM dia	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
X	3461284	X_3461284_DEL [dm3] X_3567251_DEL [dm6]	GCAACAT	TA	4.194e^-5	0.845	INTRON CG32791 & 1 other
2L	3788095	2L_3788095_SNP [dm3] 2L_3788095_SNP [dm6]	A	T	4.224e^-5	0.845	INTRON CG3921
3L	3079865	3L_3079865_SNP [dm3] 3L_3079865_SNP [dm6]	G	A	4.237e^-5	0.845	INTRON CG11486
3L	14155598	3L_14155598_SNP [dm3] 3L_14162498_SNP [dm6]	C	A	4.310e^-5	0.845	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	2278520	X_2278520_SNP [dm3] X_2384487_SNP [dm6]	G	A	4.361e^-5	0.845	SYNONYMOUS_CODING PsGEF	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	20763319	2L_20763319_SNP [dm3] 2L_20763319_SNP [dm6]	C	A	4.427e^-5	0.845	INTRON dia
3R	20331956	3R_20331956_SNP [dm3] 3R_24506234_SNP [dm6]	C	T	4.433e^-5	0.845	INTERGENIC	transposable element FlyBase
2L	19545559	2L_19545559_SNP [dm3] 2L_19545559_SNP [dm6]	C	A	4.474e^-5	0.845	UTR_3_PRIME CG10337 DOWNSTREAM ref_2_P
2L	18892949	2L_18892949_SNP [dm3] 2L_18892949_SNP [dm6]	C	T	4.518e^-5	0.845	UPSTREAM CR44737 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	16799487	3R_16799487_SNP [dm3] 3R_20973765_SNP [dm6]	T	G	4.520e^-5	0.845	INTRON Atpalpha

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Variant impact
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Phenotype distribution and association to known covariates

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GWAS results