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=2.532e^-7)
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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1213 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	25798634	3R_25798634_SNP [dm3] 3R_29972912_SNP [dm6]	C	G	2.023e^-6	0.974	INTERGENIC
3R	25798644	3R_25798644_SNP [dm3] 3R_29972922_SNP [dm6]	G	A	2.260e^-6	0.974	INTERGENIC
3R	25798645	3R_25798645_SNP [dm3] 3R_29972923_SNP [dm6]	G	C	2.260e^-6	0.974	INTERGENIC
3R	23816356	3R_23816356_SNP [dm3] 3R_27990634_SNP [dm6]	T	C	4.094e^-6	0.974	UTR_5_PRIME CG4815
3R	23816361	3R_23816361_SNP [dm3] 3R_27990639_SNP [dm6]	C	T	4.094e^-6	0.974	START_GAINED CG4815 UTR_5_PRIME CG4815
3L	12007433	3L_12007433_SNP [dm3] 3L_12014333_SNP [dm6]	A	T	5.581e^-6	0.974	INTRON rols
3L	12007537	3L_12007537_SNP [dm3] 3L_12014437_SNP [dm6]	G	A	6.574e^-6	0.974	INTRON rols
3L	12007530	3L_12007530_SNP [dm3] 3L_12014430_SNP [dm6]	C	A	7.722e^-6	0.974	INTRON rols
3R	22752598	3R_22752598_SNP [dm3] 3R_26926876_SNP [dm6]	T	C	1.279e^-5	0.974	INTRON sda
3R	13409284	3R_13409284_SNP [dm3] 3R_17583562_SNP [dm6]	C	T	1.369e^-5	0.974	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	12883434	3L_12883434_SNP [dm3] 3L_12890334_SNP [dm6]	T	C	1.510e^-5	0.974	UPSTREAM CR45748 INTRON CG43894
3R	13409285	3R_13409285_SNP [dm3] 3R_17583563_SNP [dm6]	C	G	1.698e^-5	0.974	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	12883415	3L_12883415_SNP [dm3] 3L_12890315_SNP [dm6]	T	G	2.243e^-5	0.974	UPSTREAM CR45748 INTRON CG43894
3L	12883459	3L_12883459_SNP [dm3] 3L_12890359_SNP [dm6]	T	C	2.243e^-5	0.974	SYNONYMOUS_CODING CG43894 UPSTREAM CR45748
3R	23815878	3R_23815878_SNP [dm3] 3R_27990156_SNP [dm6]	C	T	2.438e^-5	0.974	SYNONYMOUS_CODING CG4815	TF binding site mE1_TFBS_sens
2R	9837459	2R_9837459_SNP [dm3] 2R_13949954_SNP [dm6]	G	A	2.818e^-5	0.974	SYNONYMOUS_CODING AGO1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	9837501	2R_9837501_SNP [dm3] 2R_13949996_SNP [dm6]	G	A	2.818e^-5	0.974	SYNONYMOUS_CODING AGO1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	24844967	3R_24844967_SNP [dm3] 3R_29019245_SNP [dm6]	T	A	2.932e^-5	0.974	INTRON wat	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9951721	3R_9951721_SNP [dm3] 3R_14125999_SNP [dm6]	A	C	2.967e^-5	0.974	UPSTREAM 140up INTRON RpII140	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	5874296	3L_5874296_SNP [dm3] 3L_5881196_SNP [dm6]	T	G	3.244e^-5	0.974	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	19880854	2R_19880854_SNP [dm3] 2R_23993331_SNP [dm6]	T	A	3.403e^-5	0.974	UPSTREAM mir-1009 INTRON CG3860
2R	19880859	2R_19880859_SNP [dm3] 2R_23993336_SNP [dm6]	C	G	3.403e^-5	0.974	UPSTREAM mir-1009 INTRON CG3860
2R	19880863	2R_19880863_SNP [dm3] 2R_23993340_SNP [dm6]	T	A	3.438e^-5	0.974	UPSTREAM mir-1009 INTRON CG3860
3R	23815866	3R_23815866_SNP [dm3] 3R_27990144_SNP [dm6]	G	A	3.447e^-5	0.974	SYNONYMOUS_CODING CG4815	TF binding site mE1_TFBS_sens
2L	8780948	2L_8780948_SNP [dm3] 2L_8780948_SNP [dm6]	C	T	3.450e^-5	0.974	DOWNSTREAM CG42710 INTRON CG9468
2L	1838496	2L_1838496_SNP [dm3] 2L_1838496_SNP [dm6]	G	C	3.597e^-5	0.974	DOWNSTREAM CR44073 INTRON wry
2R	19882363	2R_19882363_SNP [dm3] 2R_23994840_SNP [dm6]	T	C	3.732e^-5	0.974	UTR_5_PRIME CG3860 DOWNSTREAM Unc-89
3L	12886091	3L_12886091_SNP [dm3] 3L_12892991_SNP [dm6]	A	C	3.876e^-5	0.974	DOWNSTREAM CG43894 INTRON CG14118	TF binding site mE1_TFBS_Trl
2L	1838533	2L_1838533_SNP [dm3] 2L_1838533_SNP [dm6]	A	C	4.107e^-5	0.974	DOWNSTREAM CR44073 INTRON wry
X	10191090	X_10191090_SNP [dm3] X_10297057_SNP [dm6]	C	G	4.377e^-5	0.974	INTRON alpha-Man-I
2R	9837441	2R_9837441_SNP [dm3] 2R_13949936_SNP [dm6]	A	T	4.388e^-5	0.974	SYNONYMOUS_CODING AGO1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	19138299	2L_19138299_SNP [dm3] 2L_19138299_SNP [dm6]	G	A	4.691e^-5	0.974	INTRON brat	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	9951715	3R_9951715_SNP [dm3] 3R_14125993_SNP [dm6]	T	G	4.846e^-5	0.974	UPSTREAM 140up INTRON RpII140	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	9562019	3R_9562019_SNP [dm3] 3R_13736297_SNP [dm6]	A	T	4.920e^-5	0.974	INTRON CG34383
2L	1838453	2L_1838453_SNP [dm3] 2L_1838453_SNP [dm6]	T	A	4.980e^-5	0.974	INTRON wry
2L	1838459	2L_1838459_SNP [dm3] 2L_1838459_SNP [dm6]	T	A	4.980e^-5	0.974	INTRON wry
3L	4419657	3L_4419657_SNP [dm3] 3L_4419657_SNP [dm6]	T	C	5.373e^-5	0.974	SYNONYMOUS_CODING DOR	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	20111193	2R_20111193_SNP [dm3] 2R_24223670_SNP [dm6]	C	T	5.376e^-5	0.974	INTRON CG30419
X	19072894	X_19072894_SNP [dm3] X_19178861_SNP [dm6]	A	T	5.481e^-5	0.974	INTRON CG7556
2R	8252419	2R_8252419_SNP [dm3] 2R_12364914_SNP [dm6]	G	A	5.535e^-5	0.974	EXON CR33013
2L	3216719	2L_3216719_SNP [dm3] 2L_3216719_SNP [dm6]	C	G	5.648e^-5	0.974	INTERGENIC
2R	16638857	2R_16638857_SNP [dm3] 2R_20751352_SNP [dm6]	G	T	5.679e^-5	0.974	NON_SYNONYMOUS_CODING CG34201 DOWNSTREAM dpr
3R	26666789	3R_26666789_SNP [dm3] 3R_30841067_SNP [dm6]	C	G	5.763e^-5	0.974	SYNONYMOUS_CODING CG15544	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	23299020	3R_23299020_SNP [dm3] 3R_27473298_SNP [dm6]	T	G	5.848e^-5	0.974	INTERGENIC
X	10191105	X_10191105_SNP [dm3] X_10297072_SNP [dm6]	A	G	5.868e^-5	0.974	INTRON alpha-Man-I
3R	23000795	3R_23000795_SNP [dm3] 3R_27175073_SNP [dm6]	C	A	5.886e^-5	0.974	INTRON Ser
3L	14845477	3L_14845477_SNP [dm3] 3L_14852377_SNP [dm6]	T	A	5.933e^-5	0.974	INTRON CG17839
2L	10118456	2L_10118456_SNP [dm3] 2L_10118456_SNP [dm6]	A	T	6.083e^-5	0.974	INTRON CG44153 & 1 other	transposable element FlyBase
3R	3144013	3R_3144013_SNP [dm3] 3R_7318291_SNP [dm6]	C	T	6.090e^-5	0.974	INTERGENIC
2R	13724201	2R_13724201_SNP [dm3] 2R_17836696_SNP [dm6]	T	C	6.128e^-5	0.974	INTRON grh	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	14844566	2R_14844566_SNP [dm3] 2R_18957061_SNP [dm6]	T	C	6.351e^-5	0.974	SYNONYMOUS_CODING sano	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	6734299	2R_6734299_SNP [dm3] 2R_10846794_SNP [dm6]	A	C	6.534e^-5	0.974	INTRON CG30015
3R	26666783	3R_26666783_SNP [dm3] 3R_30841061_SNP [dm6]	C	T	6.590e^-5	0.974	SYNONYMOUS_CODING CG15544	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	19270508	2R_19270508_SNP [dm3] 2R_23382985_SNP [dm6]	T	G	6.660e^-5	0.974	UPSTREAM CR44784 DOWNSTREAM yellow-d2 INTRON CG13551	TF binding site mE1_TFBS_cad
3R	18454521	3R_18454521_SNP [dm3] 3R_22628799_SNP [dm6]	A	C	6.996e^-5	0.974	UPSTREAM CR43474 INTRON loco EXON CR43475	regulatory region REDfly_CRMs
2L	6763744	2L_6763744_SNP [dm3] 2L_6763744_SNP [dm6]	C	A	7.073e^-5	0.974	NON_SYNONYMOUS_CODING CG11321	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	20245354	X_20245354_SNP [dm3] X_20374327_SNP [dm6]	A	T	7.170e^-5	0.974	INTERGENIC
3R	24816610	3R_24816610_SNP [dm3] 3R_28990888_SNP [dm6]	C	G	7.504e^-5	0.974	INTERGENIC
X	10705184	X_10705184_SNP [dm3] X_10811151_SNP [dm6]	G	C	7.514e^-5	0.974	INTRON Imp	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14557679	2R_14557679_SNP [dm3] 2R_18670174_SNP [dm6]	C	A	7.558e^-5	0.974	INTRON edl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	17818652	2R_17818652_SNP [dm3] 2R_21931147_SNP [dm6]	G	A	7.653e^-5	0.974	INTRON Fili
3R	17212628	3R_17212628_SNP [dm3] 3R_21386906_SNP [dm6]	T	A	7.822e^-5	0.974	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	27340138	3R_27340138_SNP [dm3] 3R_31514416_SNP [dm6]	T	C	7.930e^-5	0.974	INTERGENIC
3R	27340370	3R_27340370_SNP [dm3] 3R_31514648_SNP [dm6]	T	C	7.930e^-5	0.974	INTERGENIC
3R	26121059	3R_26121059_SNP [dm3] 3R_30295337_SNP [dm6]	C	T	7.958e^-5	0.974	INTRON hdc
X	19072973	X_19072973_SNP [dm3] X_19178940_SNP [dm6]	G	A	8.012e^-5	0.974	INTRON CG7556	TF binding site BDTNP1_TFBS_dl
2R	13704366	2R_13704366_SNP [dm3] 2R_17816861_SNP [dm6]	A	G	8.177e^-5	0.974	INTRON grh	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3R	19707888	3R_19707888_SNP [dm3] 3R_23882166_SNP [dm6]	C	T	8.219e^-5	0.974	INTRON Pli
3R	17212554	3R_17212554_SNP [dm3] 3R_21386832_SNP [dm6]	C	T	8.298e^-5	0.974	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA
3R	17212560	3R_17212560_SNP [dm3] 3R_21386838_SNP [dm6]	A	G	8.298e^-5	0.974	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_HSA
3R	9955109	3R_9955109_SNP [dm3] 3R_14129387_SNP [dm6]	G	A	8.344e^-5	0.974	SYNONYMOUS_CODING RpII140	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	10191091	X_10191091_SNP [dm3] X_10297058_SNP [dm6]	A	T	9.208e^-5	0.974	INTRON alpha-Man-I
2L	3772355	2L_3772355_SNP [dm3] 2L_3772355_SNP [dm6]	C	T	9.459e^-5	0.974	INTRON bowl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
2L	17705285	2L_17705285_SNP [dm3] 2L_17705285_SNP [dm6]	C	G	9.503e^-5	0.974	UTR_3_PRIME CG43231 INTRON CadN
3L	18494408	3L_18494408_SNP [dm3] 3L_18501308_SNP [dm6]	T	A	9.867e^-5	0.974	INTRON AstC-R2
3R	20132454	3R_20132454_SNP [dm3] 3R_24306732_SNP [dm6]	C	T	9.935e^-5	0.974	SYNONYMOUS_CODING crb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	6734165	2R_6734165_SNP [dm3] 2R_10846660_SNP [dm6]	C	T	9.943e^-5	0.974	INTRON CG30015
3R	27340107	3R_27340107_SNP [dm3] 3R_31514385_SNP [dm6]	A	T	1.049e^-4	0.974	INTERGENIC
3L	10066858	3L_10066858_SNP [dm3] 3L_10073758_SNP [dm6]	C	T	1.051e^-4	0.974	INTRON dpr6
3L	10066897	3L_10066897_SNP [dm3] 3L_10073797_SNP [dm6]	C	T	1.051e^-4	0.974	INTRON dpr6
3R	23405689	3R_23405689_SNP [dm3] 3R_27579967_SNP [dm6]	G	T	1.064e^-4	0.974	INTRON wdb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	3778487	2R_3778487_SNP [dm3] 2R_7890982_SNP [dm6]	C	G	1.073e^-4	0.974	INTRON CG30377
3R	18691256	3R_18691256_SNP [dm3] 3R_22865534_SNP [dm6]	T	C	1.075e^-4	0.974	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	23441267	3R_23441267_SNP [dm3] 3R_27615545_SNP [dm6]	G	A	1.076e^-4	0.974	INTRON Tusp
X	19029782	X_19029782_SNP [dm3] X_19135749_SNP [dm6]	T	C	1.078e^-4	0.974	DOWNSTREAM RhoGAP18B INTRON Obp18a
3L	13176703	3L_13176703_SNP [dm3] 3L_13183603_SNP [dm6]	A	T	1.103e^-4	0.974	INTERGENIC
3L	14845597	3L_14845597_INS [dm3] 3L_14852497_INS [dm6]	A	AA	1.108e^-4	0.974	INTRON CG17839
2R	6734224	2R_6734224_DEL [dm3] 2R_10846719_DEL [dm6]	TATTGT	T	1.108e^-4	0.974	INTRON CG30015
3L	12007278	3L_12007278_INS [dm3] 3L_12014178_INS [dm6]	G	GG	1.121e^-4	0.974	INTRON rols
3R	11467545	3R_11467545_SNP [dm3] 3R_15641823_SNP [dm6]	C	G	1.126e^-4	0.974	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	14031122	3R_14031122_SNP [dm3] 3R_18205400_SNP [dm6]	C	T	1.128e^-4	0.974	INTRON CG7985
2R	9837483	2R_9837483_SNP [dm3] 2R_13949978_SNP [dm6]	G	A	1.130e^-4	0.974	SYNONYMOUS_CODING AGO1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	18755217	3R_18755217_SNP [dm3] 3R_22929495_SNP [dm6]	T	A	1.133e^-4	0.974	INTRON klg
2R	14844378	2R_14844378_SNP [dm3] 2R_18956873_SNP [dm6]	A	C	1.134e^-4	0.974	SYNONYMOUS_CODING sano	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	20335235	X_20335235_SNP [dm3] X_20464208_SNP [dm6]	G	A	1.156e^-4	0.974	SYNONYMOUS_CODING CG32506
2R	5687275	2R_5687275_SNP [dm3] 2R_9799770_SNP [dm6]	A	C	1.164e^-4	0.974	INTRON CG1688
3L	6924977	3L_6924977_SNP [dm3] 3L_6931877_SNP [dm6]	A	T	1.201e^-4	0.974	SYNONYMOUS_CODING CG45413
3R	22715372	3R_22715372_SNP [dm3] 3R_26889650_SNP [dm6]	A	G	1.208e^-4	0.974	INTRON T48	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi
3R	9562044	3R_9562044_SNP [dm3] 3R_13736322_SNP [dm6]	A	C	1.224e^-4	0.974	INTRON CG34383
2L	8772925	2L_8772925_SNP [dm3] 2L_8772925_SNP [dm6]	C	A	1.258e^-4	0.974	UPSTREAM CG9465 DOWNSTREAM CG9466 INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

LC50_Alpha_Amanitin phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results