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=6.826e^-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

Covariate	p-value	Significance
In_2L_t	0.02068
In_3R_K	0.08074
In_3R_Mo	0.04188

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.2014	0.045
In_3R_Mo	7.6977	0.0213

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2722 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	4737896	3L_4737896_SNP [dm3] 3L_4737896_SNP [dm6]	G	A	6.356e^-7	0.451	INTRON RhoGEF64C
3L	4737895	3L_4737895_SNP [dm3] 3L_4737895_SNP [dm6]	A	G	7.636e^-7	0.451	INTRON RhoGEF64C
3L	2646080	3L_2646080_SNP [dm3] 3L_2646080_SNP [dm6]	C	T	8.647e^-7	0.451	SYNONYMOUS_CODING CG1143	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	14695058	2L_14695058_SNP [dm3] 2L_14695058_SNP [dm6]	G	A	1.182e^-6	0.451	INTERGENIC
3L	4647084	3L_4647084_INS [dm3] 3L_4647084_INS [dm6]	T	TC	1.341e^-6	0.451	INTRON axo
3L	712399	3L_712399_SNP [dm3] 3L_712399_SNP [dm6]	A	T	1.857e^-6	0.451	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	4094020	X_4094020_SNP [dm3] X_4199987_SNP [dm6]	T	C	2.140e^-6	0.451	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	712385	3L_712385_DEL [dm3] 3L_712385_DEL [dm6]	TA	T	2.162e^-6	0.451	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712376	3L_712376_SNP [dm3] 3L_712376_SNP [dm6]	G	A	2.466e^-6	0.451	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	711790	3L_711790_SNP [dm3] 3L_711790_SNP [dm6]	A	T	2.943e^-6	0.451	UTR_5_PRIME CG13896	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	24412989	3R_24412989_SNP [dm3] 3R_28587267_SNP [dm6]	T	C	3.066e^-6	0.451	EXON MRE23	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
2L	19841437	2L_19841437_SNP [dm3] 2L_19841437_SNP [dm6]	G	A	3.275e^-6	0.451	INTRON sick
3L	712388	3L_712388_DEL [dm3] 3L_712388_DEL [dm6]	AAT	A	3.314e^-6	0.451	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712384	3L_712384_SNP [dm3] 3L_712384_SNP [dm6]	T	C	3.370e^-6	0.451	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3R	25570656	3R_25570656_SNP [dm3] 3R_29744934_SNP [dm6]	G	A	4.394e^-6	0.479	SYNONYMOUS_CODING CG7609 UPSTREAM IntS11	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	14694914	2L_14694914_SNP [dm3] 2L_14694914_SNP [dm6]	C	T	4.679e^-6	0.479	INTERGENIC
3L	712235	3L_712235_SNP [dm3] 3L_712235_SNP [dm6]	C	T	5.313e^-6	0.479	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
3L	712423	3L_712423_SNP [dm3] 3L_712423_SNP [dm6]	G	C	5.521e^-6	0.479	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
2L	19808957	2L_19808957_SNP [dm3] 2L_19808957_SNP [dm6]	T	A	5.526e^-6	0.479	INTRON sick	TF binding site mE1_TFBS_cad
3L	712348	3L_712348_SNP [dm3] 3L_712348_SNP [dm6]	G	T	5.563e^-6	0.479	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	21160839	X_21160839_SNP [dm3] X_21289812_SNP [dm6]	T	C	5.742e^-6	0.479	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	712377	3L_712377_SNP [dm3] 3L_712377_SNP [dm6]	A	C	6.197e^-6	0.479	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3R	24485802	3R_24485802_SNP [dm3] 3R_28660080_SNP [dm6]	A	G	6.502e^-6	0.479	INTERGENIC
3L	13487564	3L_13487564_SNP [dm3] 3L_13494464_SNP [dm6]	G	T	6.530e^-6	0.479	INTRON Tgi	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
3R	24413164	3R_24413164_SNP [dm3] 3R_28587442_SNP [dm6]	C	T	7.186e^-6	0.479	EXON MRE23	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	13570329	3R_13570329_SNP [dm3] 3R_17744607_SNP [dm6]	A	C	7.412e^-6	0.479	INTRON TyrRII	TF binding site mE1_TFBS_cad
3L	412583	3L_412583_SNP [dm3] 3L_412583_SNP [dm6]	G	T	7.422e^-6	0.479	INTERGENIC
3L	4737859	3L_4737859_SNP [dm3] 3L_4737859_SNP [dm6]	A	G	7.570e^-6	0.479	INTRON RhoGEF64C
3R	15077609	3R_15077609_SNP [dm3] 3R_19251887_SNP [dm6]	C	A	7.729e^-6	0.479	INTERGENIC
X	10543785	X_10543785_SNP [dm3] X_10649752_SNP [dm6]	T	C	7.820e^-6	0.479	INTRON X11Lbeta
2L	19840286	2L_19840286_SNP [dm3] 2L_19840286_SNP [dm6]	C	A	7.922e^-6	0.479	INTRON sick
3L	711857	3L_711857_SNP [dm3] 3L_711857_SNP [dm6]	A	C	8.521e^-6	0.485	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	5709131	3R_5709131_SNP [dm3] 3R_9883409_SNP [dm6]	C	G	8.537e^-6	0.485	INTRON Glut4EF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	712337	3L_712337_SNP [dm3] 3L_712337_SNP [dm6]	G	T	8.978e^-6	0.495	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
2L	14695099	2L_14695099_SNP [dm3] 2L_14695099_SNP [dm6]	A	C	9.337e^-6	0.5	INTERGENIC
3L	16896011	3L_16896011_SNP [dm3] 3L_16902911_SNP [dm6]	A	T	9.637e^-6	0.501	NON_SYNONYMOUS_CODING Lmpt INTRON Lmpt	TF binding site mE1_TFBS_chinmo
3L	712226	3L_712226_SNP [dm3] 3L_712226_SNP [dm6]	C	A	1.112e^-5	0.501	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Ubx mE1_TFBS_zfh1
2L	19835455	2L_19835455_SNP [dm3] 2L_19835455_SNP [dm6]	A	C	1.148e^-5	0.501	INTRON sick
3R	12970762	3R_12970762_SNP [dm3] 3R_17145040_SNP [dm6]	A	T	1.150e^-5	0.501	UTR_3_PRIME m-cup DOWNSTREAM m-cup
3L	4737892	3L_4737892_SNP [dm3] 3L_4737892_SNP [dm6]	T	C	1.169e^-5	0.501	INTRON RhoGEF64C
3L	712374	3L_712374_SNP [dm3] 3L_712374_SNP [dm6]	G	C	1.199e^-5	0.501	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	8207850	3L_8207850_SNP [dm3] 3L_8214750_SNP [dm6]	T	C	1.215e^-5	0.501	UPSTREAM CG8012 INTERGENIC
X	21160844	X_21160844_SNP [dm3] X_21289817_SNP [dm6]	G	C	1.217e^-5	0.501	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	24413609	3R_24413609_SNP [dm3] 3R_28587887_SNP [dm6]	C	T	1.220e^-5	0.501	EXON MRE23	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	8134266	2R_8134266_SNP [dm3] 2R_12246761_SNP [dm6]	C	T	1.254e^-5	0.501	EXON CR44315
X	4093939	X_4093939_SNP [dm3] X_4199906_SNP [dm6]	A	C	1.260e^-5	0.501	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
X	9638379	X_9638379_SNP [dm3] X_9744346_SNP [dm6]	T	C	1.278e^-5	0.501	INTRON Sp1	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	17696524	2R_17696524_SNP [dm3] 2R_21809019_SNP [dm6]	T	C	1.307e^-5	0.501	INTERGENIC
3L	677700	3L_677700_SNP [dm3] 3L_677700_SNP [dm6]	T	A	1.348e^-5	0.501	DOWNSTREAM CG17129 INTERGENIC
3L	7479975	3L_7479975_SNP [dm3] 3L_7486875_SNP [dm6]	T	C	1.377e^-5	0.501	SYNONYMOUS_CODING mthl6	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	13549841	3L_13549841_SNP [dm3] 3L_13556741_SNP [dm6]	A	G	1.388e^-5	0.501	INTRON bru-3
3L	712335	3L_712335_SNP [dm3] 3L_712335_SNP [dm6]	T	A	1.396e^-5	0.501	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3R	2868309	3R_2868309_SNP [dm3] 3R_7042587_SNP [dm6]	G	A	1.435e^-5	0.501	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	11809705	2R_11809705_SNP [dm3] 2R_15922200_SNP [dm6]	G	A	1.444e^-5	0.501	UPSTREAM sli DOWNSTREAM bdg INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_bab1 mE1_TFBS_HSA
3R	2868311	3R_2868311_INS [dm3] 3R_7042589_INS [dm6]	C	CGGA	1.504e^-5	0.513	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	413912	3L_413912_SNP [dm3] 3L_413912_SNP [dm6]	C	T	1.673e^-5	0.555	INTERGENIC	TF binding site mE1_TFBS_Kr
3L	2645866	3L_2645866_SNP [dm3] 3L_2645866_SNP [dm6]	A	G	1.687e^-5	0.555	SYNONYMOUS_CODING CG1143	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12792346	3L_12792346_SNP [dm3] 3L_12799246_SNP [dm6]	G	C	1.751e^-5	0.566	INTRON Atg1
2L	19802428	2L_19802428_SNP [dm3] 2L_19802428_SNP [dm6]	A	G	1.785e^-5	0.567	INTRON sick
2L	387696	2L_387696_SNP [dm3] 2L_387696_SNP [dm6]	T	A	1.864e^-5	0.575	DOWNSTREAM al INTERGENIC
2R	6016574	2R_6016574_SNP [dm3] 2R_10129069_SNP [dm6]	G	A	1.888e^-5	0.575	INTRON gem	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	15428091	2R_15428091_SNP [dm3] 2R_19540586_SNP [dm6]	C	A	1.919e^-5	0.575	INTRON sm
X	17952248	X_17952248_SNP [dm3] X_18058215_SNP [dm6]	C	A	1.982e^-5	0.575	INTRON Sh
X	4093930	X_4093930_SNP [dm3] X_4199897_SNP [dm6]	T	C	1.995e^-5	0.575	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
X	9287766	X_9287766_SNP [dm3] X_9393733_SNP [dm6]	T	C	2.048e^-5	0.575	INTRON mgl	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	13136787	X_13136787_SNP [dm3] X_13242754_SNP [dm6]	C	T	2.176e^-5	0.575	INTRON mew	TF binding site BDTNP1_TFBS_da
X	20215260	X_20215260_SNP [dm3] X_20344233_SNP [dm6]	A	C	2.188e^-5	0.575	INTERGENIC	transposable element FlyBase
3L	13339531	3L_13339531_SNP [dm3] 3L_13346431_SNP [dm6]	G	T	2.200e^-5	0.575	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	3469607	3R_3469607_SNP [dm3] 3R_7643885_SNP [dm6]	C	T	2.208e^-5	0.575	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	16289150	2R_16289150_SNP [dm3] 2R_20401645_SNP [dm6]	G	A	2.232e^-5	0.575	INTERGENIC
2L	2021719	2L_2021719_SNP [dm3] 2L_2021719_SNP [dm6]	G	A	2.243e^-5	0.575	INTRON CG4238
3L	12792354	3L_12792354_SNP [dm3] 3L_12799254_SNP [dm6]	T	G	2.269e^-5	0.575	INTRON Atg1
2R	8133682	2R_8133682_SNP [dm3] 2R_12246177_SNP [dm6]	T	A	2.341e^-5	0.575	DOWNSTREAM CR44315 INTERGENIC
2R	2957893	2R_2957893_SNP [dm3] 2R_7070388_SNP [dm6]	A	C	2.361e^-5	0.575	UPSTREAM tRNA:CR30298 DOWNSTREAM CG12831 & 2 others INTERGENIC
3L	3966618	3L_3966618_DEL [dm3] 3L_3966618_DEL [dm6]	CCGCTGTCC	C	2.367e^-5	0.575	INTERGENIC
2L	13626041	2L_13626041_SNP [dm3] 2L_13626041_SNP [dm6]	G	A	2.375e^-5	0.575	INTRON kuz
X	17952250	X_17952250_SNP [dm3] X_18058217_SNP [dm6]	G	A	2.426e^-5	0.575	INTRON Sh
3R	14972052	3R_14972052_SNP [dm3] 3R_19146330_SNP [dm6]	A	G	2.437e^-5	0.575	INTRON Ppcs
3L	16725723	3L_16725723_SNP [dm3] 3L_16732623_SNP [dm6]	C	G	2.494e^-5	0.575	UPSTREAM CG9701 INTERGENIC
X	5228937	X_5228937_INS [dm3] X_5334904_INS [dm6]	C	CTACACTCGCAAAAAAAAAA...	2.512e^-5	0.575	DOWNSTREAM CanB INTERGENIC
3R	24353994	3R_24353994_SNP [dm3] 3R_28528272_SNP [dm6]	G	A	2.515e^-5	0.575	NON_SYNONYMOUS_CODING Ppn	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	5160275	2L_5160275_SNP [dm3] 2L_5160275_SNP [dm6]	T	G	2.517e^-5	0.575	SYNONYMOUS_CODING Msp300 INTRON Msp300	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	4400876	3R_4400876_INS [dm3] 3R_8575154_INS [dm6]	T	TT	2.610e^-5	0.583	INTERGENIC
2R	8144116	2R_8144116_SNP [dm3] 2R_12256611_SNP [dm6]	T	C	2.663e^-5	0.583	UPSTREAM Vha36-2 DOWNSTREAM CG13168 INTERGENIC
3R	25570751	3R_25570751_SNP [dm3] 3R_29745029_SNP [dm6]	A	C	2.681e^-5	0.583	START_GAINED CG7609 UTR_5_PRIME CG7609 UPSTREAM IntS11	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	14689608	2L_14689608_SNP [dm3] 2L_14689608_SNP [dm6]	A	G	2.711e^-5	0.583	UPSTREAM osp INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	8447265	2L_8447265_SNP [dm3] 2L_8447265_SNP [dm6]	A	G	2.752e^-5	0.583	NON_SYNONYMOUS_CODING U26 UTR_3_PRIME U26	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	19837577	2L_19837577_SNP [dm3] 2L_19837577_SNP [dm6]	G	A	2.754e^-5	0.583	INTRON sick	TF binding site mE1_TFBS_cad
2R	8144149	2R_8144149_SNP [dm3] 2R_12256644_SNP [dm6]	T	A	2.767e^-5	0.583	UPSTREAM Vha36-2 DOWNSTREAM CG13168 INTERGENIC
X	13137037	X_13137037_SNP [dm3] X_13243004_SNP [dm6]	C	T	2.816e^-5	0.587	INTRON mew	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	15428084	2R_15428084_SNP [dm3] 2R_19540579_SNP [dm6]	A	G	2.908e^-5	0.587	INTRON sm
2L	2021720	2L_2021720_SNP [dm3] 2L_2021720_SNP [dm6]	T	A	2.943e^-5	0.587	INTRON CG4238
2L	17289541	2L_17289541_SNP [dm3] 2L_17289541_SNP [dm6]	C	T	2.943e^-5	0.587	INTERGENIC
X	13137038	X_13137038_SNP [dm3] X_13243005_SNP [dm6]	A	G	2.944e^-5	0.587	INTRON mew	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	712343	3L_712343_SNP [dm3] 3L_712343_SNP [dm6]	A	C	3.005e^-5	0.587	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	15483333	3L_15483333_SNP [dm3] 3L_15490233_SNP [dm6]	T	C	3.077e^-5	0.587	INTERGENIC
2L	19941325	2L_19941325_SNP [dm3] 2L_19941325_SNP [dm6]	C	T	3.085e^-5	0.587	INTRON sick	TF binding site mE1_TFBS_cad mE1_TFBS_Kr
3L	712319	3L_712319_INS [dm3] 3L_712319_INS [dm6]	C	CA	3.103e^-5	0.587	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	712342	3L_712342_SNP [dm3] 3L_712342_SNP [dm6]	A	T	3.103e^-5	0.587	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
3L	837693	3L_837693_SNP [dm3] 3L_837693_SNP [dm6]	A	C	3.213e^-5	0.587	UPSTREAM CG13887 & 1 other DOWNSTREAM CG42554 INTRON CG13901	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA

Showing 1 to 100 of 1,000 entries

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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=3.590e^-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

Covariate	p-value	Significance
In_2L_t	0.04742
In_3R_K	0.08720

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	5.2719	0.0717
In_3R_K	5.5609	0.062
In_3R_Mo	5.8878	0.0527

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2578 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	2646080	3L_2646080_SNP [dm3] 3L_2646080_SNP [dm6]	C	T	5.314e^-8	0.1	SYNONYMOUS_CODING CG1143	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	5115825	X_5115825_SNP [dm3] X_5221792_SNP [dm6]	A	G	6.297e^-7	0.384	INTRON CG15465 & 1 other
2L	15281202	2L_15281202_DEL [dm3] 2L_15281202_DEL [dm6]	CC	T	7.360e^-7	0.384	DOWNSTREAM CR45349 INTERGENIC
3L	4737896	3L_4737896_SNP [dm3] 3L_4737896_SNP [dm6]	G	A	9.292e^-7	0.384	INTRON RhoGEF64C
X	21160839	X_21160839_SNP [dm3] X_21289812_SNP [dm6]	T	C	1.025e^-6	0.384	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	4737895	3L_4737895_SNP [dm3] 3L_4737895_SNP [dm6]	A	G	1.246e^-6	0.389	INTRON RhoGEF64C
X	21160844	X_21160844_SNP [dm3] X_21289817_SNP [dm6]	G	C	2.567e^-6	0.649	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	9638379	X_9638379_SNP [dm3] X_9744346_SNP [dm6]	T	C	3.319e^-6	0.649	INTRON Sp1	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	13570329	3R_13570329_SNP [dm3] 3R_17744607_SNP [dm6]	A	C	3.480e^-6	0.649	INTRON TyrRII	TF binding site mE1_TFBS_cad
3L	7479975	3L_7479975_SNP [dm3] 3L_7486875_SNP [dm6]	T	C	3.723e^-6	0.649	SYNONYMOUS_CODING mthl6	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	4647084	3L_4647084_INS [dm3] 3L_4647084_INS [dm6]	T	TC	3.809e^-6	0.649	INTRON axo
X	21063578	X_21063578_SNP [dm3] X_21192551_SNP [dm6]	G	A	4.791e^-6	0.666	UPSTREAM CG14579 INTERGENIC
2L	13626041	2L_13626041_SNP [dm3] 2L_13626041_SNP [dm6]	G	A	5.457e^-6	0.666	INTRON kuz
3L	6100199	3L_6100199_SNP [dm3] 3L_6107099_SNP [dm6]	C	T	5.573e^-6	0.666	INTRON Ets65A	TF binding site mE1_TFBS_cad
X	10543785	X_10543785_SNP [dm3] X_10649752_SNP [dm6]	T	C	5.761e^-6	0.666	INTRON X11Lbeta
3L	12792354	3L_12792354_SNP [dm3] 3L_12799254_SNP [dm6]	T	G	6.162e^-6	0.666	INTRON Atg1
3L	4737859	3L_4737859_SNP [dm3] 3L_4737859_SNP [dm6]	A	G	6.758e^-6	0.666	INTRON RhoGEF64C
X	2926734	X_2926734_SNP [dm3] X_3032701_SNP [dm6]	C	A	6.850e^-6	0.666	INTRON kirre
2L	15281222	2L_15281222_SNP [dm3] 2L_15281222_SNP [dm6]	A	G	7.117e^-6	0.666	DOWNSTREAM CR45349 INTERGENIC
X	2926031	X_2926031_SNP [dm3] X_3031998_SNP [dm6]	C	A	7.401e^-6	0.666	INTRON kirre
3L	12615746	3L_12615746_MNP [dm3] 3L_12622646_MNP [dm6]	GAA	AGC	7.510e^-6	0.666	DOWNSTREAM caup INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	12792346	3L_12792346_SNP [dm3] 3L_12799246_SNP [dm6]	G	C	8.076e^-6	0.666	INTRON Atg1
2R	4950454	2R_4950454_SNP [dm3] 2R_9062949_SNP [dm6]	G	A	8.277e^-6	0.666	INTRON ana	regulatory region REDfly_CRMs
X	4764291	X_4764291_SNP [dm3] X_4870258_SNP [dm6]	T	C	8.815e^-6	0.666	INTRON CG42594
3R	5709131	3R_5709131_SNP [dm3] 3R_9883409_SNP [dm6]	C	G	9.405e^-6	0.666	INTRON Glut4EF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	12971257	3R_12971257_SNP [dm3] 3R_17145535_SNP [dm6]	A	C	9.585e^-6	0.666	UTR_3_PRIME m-cup	TF binding site mE1_TFBS_cad
3R	12971260	3R_12971260_DEL [dm3] 3R_17145538_DEL [dm6]	AGGTAAGCATCCTA...	G	9.585e^-6	0.666	UTR_3_PRIME m-cup	TF binding site mE1_TFBS_cad
2L	14689608	2L_14689608_SNP [dm3] 2L_14689608_SNP [dm6]	A	G	1.022e^-5	0.667	UPSTREAM osp INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	15743118	2R_15743118_SNP [dm3] 2R_19855613_SNP [dm6]	T	C	1.098e^-5	0.667	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	551174	3L_551174_SNP [dm3] 3L_551174_SNP [dm6]	T	A	1.139e^-5	0.667	INTRON hipk	TF binding site BDTNP1_TFBS_dl
X	9778558	X_9778558_SNP [dm3] X_9884525_SNP [dm6]	T	A	1.155e^-5	0.667	SYNONYMOUS_CODING CG9691 DOWNSTREAM CG9689
X	13828560	X_13828560_SNP [dm3] X_13934527_SNP [dm6]	C	A	1.178e^-5	0.667	INTRON mamo	TF binding site mE1_TFBS_HSA
X	1931082	X_1931082_SNP [dm3] X_2037049_SNP [dm6]	A	G	1.178e^-5	0.667	UPSTREAM Actn INTRON Actn	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	428271	3L_428271_SNP [dm3] 3L_428271_SNP [dm6]	T	A	1.233e^-5	0.667	INTERGENIC
2L	14695058	2L_14695058_SNP [dm3] 2L_14695058_SNP [dm6]	G	A	1.245e^-5	0.667	INTERGENIC
3L	412583	3L_412583_SNP [dm3] 3L_412583_SNP [dm6]	G	T	1.355e^-5	0.698	INTERGENIC
3L	6100247	3L_6100247_SNP [dm3] 3L_6107147_SNP [dm6]	C	T	1.402e^-5	0.698	INTRON Ets65A	TF binding site mE1_TFBS_cad
3L	12615738	3L_12615738_SNP [dm3] 3L_12622638_SNP [dm6]	C	G	1.434e^-5	0.698	DOWNSTREAM caup INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	21930162	X_21930162_SNP [dm3] X_22528326_SNP [dm6]	C	T	1.585e^-5	0.698	SYNONYMOUS_CODING CG17600
3L	7479886	3L_7479886_SNP [dm3] 3L_7486786_SNP [dm6]	C	T	1.626e^-5	0.698	INTRON mthl6	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	16289150	2R_16289150_SNP [dm3] 2R_20401645_SNP [dm6]	G	A	1.745e^-5	0.698	INTERGENIC
2R	9147422	2R_9147422_SNP [dm3] 2R_13259917_SNP [dm6]	A	T	1.851e^-5	0.698	UPSTREAM CG42319 INTERGENIC
X	2814871	X_2814871_INS [dm3] X_2920838_INS [dm6]	T	TTT	1.865e^-5	0.698	INTRON kirre & 1 other
X	2814875	X_2814875_SNP [dm3] X_2920842_SNP [dm6]	T	C	1.865e^-5	0.698	INTRON kirre & 1 other
2L	13720507	2L_13720507_SNP [dm3] 2L_13720507_SNP [dm6]	G	T	1.877e^-5	0.698	INTERGENIC
2R	9147438	2R_9147438_SNP [dm3] 2R_13259933_SNP [dm6]	G	A	1.945e^-5	0.698	UPSTREAM CG42319 INTERGENIC
2L	15281172	2L_15281172_SNP [dm3] 2L_15281172_SNP [dm6]	G	A	1.973e^-5	0.698	DOWNSTREAM CR45349 INTERGENIC
3R	11322549	3R_11322549_SNP [dm3] 3R_15496827_SNP [dm6]	T	C	1.976e^-5	0.698	INTERGENIC
2L	19802428	2L_19802428_SNP [dm3] 2L_19802428_SNP [dm6]	A	G	1.980e^-5	0.698	INTRON sick
2L	12260510	2L_12260510_SNP [dm3] 2L_12260510_SNP [dm6]	T	C	2.063e^-5	0.698	INTRON aret
2R	6588312	2R_6588312_SNP [dm3] 2R_10700807_SNP [dm6]	G	C	2.093e^-5	0.698	INTRON stan
2L	14702724	2L_14702724_SNP [dm3] 2L_14702724_SNP [dm6]	C	G	2.200e^-5	0.698	INTERGENIC
2R	11576547	2R_11576547_SNP [dm3] 2R_15689042_SNP [dm6]	A	G	2.204e^-5	0.698	UPSTREAM CG30090 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	22306203	2L_22306203_SNP [dm3] 2L_22306203_SNP [dm6]	T	C	2.219e^-5	0.698	INTERGENIC
2R	12696827	2R_12696827_SNP [dm3] 2R_16809322_SNP [dm6]	C	A	2.372e^-5	0.698	INTERGENIC
3L	502675	3L_502675_SNP [dm3] 3L_502675_SNP [dm6]	T	C	2.429e^-5	0.698	INTRON klar
3L	4737892	3L_4737892_SNP [dm3] 3L_4737892_SNP [dm6]	T	C	2.460e^-5	0.698	INTRON RhoGEF64C
3R	4400876	3R_4400876_INS [dm3] 3R_8575154_INS [dm6]	T	TT	2.502e^-5	0.698	INTERGENIC
3L	7480613	3L_7480613_SNP [dm3] 3L_7487513_SNP [dm6]	A	G	2.505e^-5	0.698	INTRON mthl6
2L	15031960	2L_15031960_SNP [dm3] 2L_15031960_SNP [dm6]	T	G	2.519e^-5	0.698	UPSTREAM CG31832 INTRON GABA-B-R1
2R	11330036	2R_11330036_SNP [dm3] 2R_15442531_SNP [dm6]	G	C	2.561e^-5	0.698	INTRON CG43729
2R	6588137	2R_6588137_SNP [dm3] 2R_10700632_SNP [dm6]	C	T	2.578e^-5	0.698	INTRON stan
3L	21386998	3L_21386998_SNP [dm3] 3L_21393898_SNP [dm6]	G	A	2.628e^-5	0.698	INTRON rgn
2L	7025296	2L_7025296_SNP [dm3] 2L_7025296_SNP [dm6]	C	A	2.645e^-5	0.698	NON_SYNONYMOUS_CODING CG31908	TF binding site mE1_TFBS_cad
2L	19802421	2L_19802421_SNP [dm3] 2L_19802421_SNP [dm6]	A	C	2.690e^-5	0.698	INTRON sick
3L	952114	3L_952114_SNP [dm3] 3L_952114_SNP [dm6]	T	C	2.707e^-5	0.698	INTRON Glut1
2L	1604344	2L_1604344_SNP [dm3] 2L_1604344_SNP [dm6]	G	A	2.717e^-5	0.698	SPLICE_SITE_REGION haf INTRON CG31935 & 1 other
2R	15459606	2R_15459606_SNP [dm3] 2R_19572101_SNP [dm6]	T	G	2.749e^-5	0.698	INTRON sm
X	9775935	X_9775935_SNP [dm3] X_9881902_SNP [dm6]	C	T	2.791e^-5	0.698	UPSTREAM CG9689 INTERGENIC	TF binding site mE1_TFBS_Trl
3R	5137887	3R_5137887_SNP [dm3] 3R_9312165_SNP [dm6]	A	G	2.817e^-5	0.698	INTRON CG8861
3L	7480667	3L_7480667_SNP [dm3] 3L_7487567_SNP [dm6]	A	G	2.923e^-5	0.698	SYNONYMOUS_CODING mthl6
2R	9147435	2R_9147435_SNP [dm3] 2R_13259930_SNP [dm6]	T	A	2.962e^-5	0.698	UPSTREAM CG42319 INTERGENIC
3R	25973021	3R_25973021_SNP [dm3] 3R_30147299_SNP [dm6]	T	C	2.985e^-5	0.698	INTRON AdoR
3L	22701905	3L_22701905_SNP [dm3] 3L_22708805_SNP [dm6]	C	A	2.991e^-5	0.698	INTERGENIC
X	4094020	X_4094020_SNP [dm3] X_4199987_SNP [dm6]	T	C	3.040e^-5	0.698	INTRON Fas2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	378373	2L_378373_SNP [dm3] 2L_378373_SNP [dm6]	A	T	3.079e^-5	0.698	UTR_5_PRIME al	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_Trl
2L	8452388	2L_8452388_SNP [dm3] 2L_8452388_SNP [dm6]	G	T	3.083e^-5	0.698	UPSTREAM fu12 INTRON fu12
3R	2868311	3R_2868311_INS [dm3] 3R_7042589_INS [dm6]	C	CGGA	3.107e^-5	0.698	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	11330161	2R_11330161_SNP [dm3] 2R_15442656_SNP [dm6]	G	A	3.119e^-5	0.698	INTRON CG43729
3R	12970762	3R_12970762_SNP [dm3] 3R_17145040_SNP [dm6]	A	T	3.172e^-5	0.698	UTR_3_PRIME m-cup DOWNSTREAM m-cup
2L	4512888	2L_4512888_SNP [dm3] 2L_4512888_SNP [dm6]	G	A	3.222e^-5	0.698	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12896052	2L_12896052_SNP [dm3] 2L_12896052_SNP [dm6]	T	C	3.272e^-5	0.698	INTERGENIC
3L	14811233	3L_14811233_SNP [dm3] 3L_14818133_SNP [dm6]	C	T	3.304e^-5	0.698	INTRON CG17839
2R	13950559	2R_13950559_SNP [dm3] 2R_18063054_SNP [dm6]	A	T	3.353e^-5	0.698	INTRON CG34386
3L	14561384	3L_14561384_SNP [dm3] 3L_14568284_SNP [dm6]	G	A	3.363e^-5	0.698	DOWNSTREAM CG42758 INTERGENIC
X	17321363	X_17321363_SNP [dm3] X_17427330_SNP [dm6]	A	C	3.440e^-5	0.698	INTRON CG12994 & 1 other	TF binding site mE1_TFBS_D
X	18659700	X_18659700_SNP [dm3] X_18765667_SNP [dm6]	A	T	3.454e^-5	0.698	INTRON CCKLR-17D3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	387696	2L_387696_SNP [dm3] 2L_387696_SNP [dm6]	T	A	3.468e^-5	0.698	DOWNSTREAM al INTERGENIC
3L	14817336	3L_14817336_SNP [dm3] 3L_14824236_SNP [dm6]	G	A	3.505e^-5	0.698	INTRON CG17839
3L	12148122	3L_12148122_SNP [dm3] 3L_12155022_SNP [dm6]	C	T	3.511e^-5	0.698	SYNONYMOUS_CODING Nrx-IV	TF binding site mE1_TFBS_sens
3L	4737951	3L_4737951_SNP [dm3] 3L_4737951_SNP [dm6]	C	A	3.559e^-5	0.698	INTRON RhoGEF64C
X	21930168	X_21930168_SNP [dm3] X_22528332_SNP [dm6]	T	G	3.706e^-5	0.698	SYNONYMOUS_CODING CG17600
3R	17942119	3R_17942119_SNP [dm3] 3R_22116397_SNP [dm6]	G	C	3.739e^-5	0.698	NON_SYNONYMOUS_CODING Ir94b
3R	24485802	3R_24485802_SNP [dm3] 3R_28660080_SNP [dm6]	A	G	3.800e^-5	0.698	INTERGENIC
X	8291487	X_8291487_SNP [dm3] X_8397454_SNP [dm6]	T	A	3.857e^-5	0.698	UTR_3_PRIME CG15345
2R	6588083	2R_6588083_SNP [dm3] 2R_10700578_SNP [dm6]	G	C	3.882e^-5	0.698	INTRON stan
3L	6100265	3L_6100265_SNP [dm3] 3L_6107165_SNP [dm6]	C	T	3.886e^-5	0.698	INTRON Ets65A	TF binding site mE1_TFBS_cad
2R	9147155	2R_9147155_SNP [dm3] 2R_13259650_SNP [dm6]	A	T	3.911e^-5	0.698	UPSTREAM CG42319 INTERGENIC	transposable element FlyBase
3L	6100256	3L_6100256_SNP [dm3] 3L_6107156_SNP [dm6]	A	C	4.040e^-5	0.698	INTRON Ets65A	TF binding site mE1_TFBS_cad
3L	12615764	3L_12615764_SNP [dm3] 3L_12622664_SNP [dm6]	T	A	4.056e^-5	0.698	DOWNSTREAM caup INTERGENIC	TF binding site BDTNP1_TFBS_twi

Showing 1 to 100 of 1,000 entries

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By genomic position
Variant impact
Gene name

Wing_Width phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results