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=2.979e^-3)
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_2R_NS	0.08186

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1852 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	17524798	2L_17524798_SNP [dm3] 2L_17524798_SNP [dm6]	A	G	1.132e^-6	0.621	SYNONYMOUS_CODING Dhc36C UPSTREAM CG15143 DOWNSTREAM CG15144
3R	15617697	3R_15617697_INS [dm3] 3R_19791975_INS [dm6]	C	CAAAGACACTAGAATATATA...	1.604e^-6	0.621	DOWNSTREAM tRNA:CR31215 INTERGENIC
3L	7196238	3L_7196238_SNP [dm3] 3L_7203138_SNP [dm6]	A	T	1.826e^-6	0.621	INTERGENIC
3L	7196239	3L_7196239_SNP [dm3] 3L_7203139_SNP [dm6]	T	G	1.826e^-6	0.621	INTERGENIC
3R	13915258	3R_13915258_SNP [dm3] 3R_18089536_SNP [dm6]	T	A	3.015e^-6	0.621	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	7196253	3L_7196253_SNP [dm3] 3L_7203153_SNP [dm6]	C	G	3.414e^-6	0.621	INTERGENIC
2L	4894990	2L_4894990_SNP [dm3] 2L_4894990_SNP [dm6]	C	T	4.321e^-6	0.621	INTRON CG3036
X	3378342	X_3378342_SNP [dm3] X_3484309_SNP [dm6]	A	T	4.517e^-6	0.621	NON_SYNONYMOUS_CODING CG10802 DOWNSTREAM CG14270 INTRON CR44999
3R	15617014	3R_15617014_SNP [dm3] 3R_19791292_SNP [dm6]	C	T	4.566e^-6	0.621	DOWNSTREAM tRNA:CR31215 INTERGENIC
3R	21360563	3R_21360563_SNP [dm3] 3R_25534841_SNP [dm6]	T	A	4.835e^-6	0.621	INTRON msi
X	11407530	X_11407530_SNP [dm3] X_11513497_SNP [dm6]	T	G	4.879e^-6	0.621	INTRON Drak
X	10839811	X_10839811_SNP [dm3] X_10945778_SNP [dm6]	A	G	4.944e^-6	0.621	SYNONYMOUS_CODING Myo10A	TF binding site mE1_TFBS_chinmo
3L	7196251	3L_7196251_SNP [dm3] 3L_7203151_SNP [dm6]	C	T	5.528e^-6	0.621	INTERGENIC
3R	9698947	3R_9698947_SNP [dm3] 3R_13873225_SNP [dm6]	G	T	5.681e^-6	0.621	INTRON E5	TF binding site mE1_TFBS_cad
3R	21547447	3R_21547447_SNP [dm3] 3R_25721725_SNP [dm6]	T	A	5.725e^-6	0.621	INTRON LpR2
3L	7196204	3L_7196204_SNP [dm3] 3L_7203104_SNP [dm6]	T	C	5.743e^-6	0.621	INTERGENIC
X	10839972	X_10839972_SNP [dm3] X_10945939_SNP [dm6]	G	T	5.762e^-6	0.621	NON_SYNONYMOUS_CODING Myo10A	TF binding site mE1_TFBS_chinmo
3L	7196245	3L_7196245_SNP [dm3] 3L_7203145_SNP [dm6]	G	A	5.960e^-6	0.621	INTERGENIC
2L	9422422	2L_9422422_SNP [dm3] 2L_9422422_SNP [dm6]	C	T	6.329e^-6	0.624	INTRON Mco1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	16042737	3L_16042737_SNP [dm3] 3L_16049637_SNP [dm6]	G	T	6.736e^-6	0.631	INTRON th EXON CR43951	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3R	17631419	3R_17631419_SNP [dm3] 3R_21805697_SNP [dm6]	A	T	7.693e^-6	0.65	INTRON CASK
3L	953139	3L_953139_SNP [dm3] 3L_953139_SNP [dm6]	A	T	8.050e^-6	0.65	INTRON Glut1
3L	16042724	3L_16042724_SNP [dm3] 3L_16049624_SNP [dm6]	G	A	8.134e^-6	0.65	INTRON th EXON CR43951	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
2L	16785875	2L_16785875_SNP [dm3] 2L_16785875_SNP [dm6]	A	G	8.317e^-6	0.65	INTRON Mhc	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2R	15432969	2R_15432969_SNP [dm3] 2R_19545464_SNP [dm6]	A	T	8.687e^-6	0.651	INTRON sm	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	17041018	3R_17041018_SNP [dm3] 3R_21215296_SNP [dm6]	G	T	9.663e^-6	0.697	INTRON CG5862	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2L	16786286	2L_16786286_SNP [dm3] 2L_16786286_SNP [dm6]	C	T	1.026e^-5	0.704	SYNONYMOUS_CODING Mhc	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	4112215	3L_4112215_SNP [dm3] 3L_4112215_SNP [dm6]	C	T	1.052e^-5	0.704	SYNONYMOUS_CODING Ack	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13787187	3L_13787187_SNP [dm3] 3L_13794087_SNP [dm6]	G	A	1.119e^-5	0.711	INTRON bru-3
2L	8588872	2L_8588872_SNP [dm3] 2L_8588872_SNP [dm6]	A	G	1.138e^-5	0.711	INTRON Sema-1a	TF binding site BDTNP1_TFBS_dl
3L	9390772	3L_9390772_SNP [dm3] 3L_9397672_SNP [dm6]	C	T	1.267e^-5	0.766	INTRON CG4080	TF binding site BDTNP1_TFBS_dl
3L	10981177	3L_10981177_SNP [dm3] 3L_10988077_SNP [dm6]	A	G	1.344e^-5	0.771	INTRON klu
3R	9708144	3R_9708144_SNP [dm3] 3R_13882422_SNP [dm6]	G	C	1.357e^-5	0.771	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
X	20022052	X_20022052_SNP [dm3] X_20128019_SNP [dm6]	G	A	1.495e^-5	0.795	INTERGENIC
3R	9698948	3R_9698948_SNP [dm3] 3R_13873226_SNP [dm6]	C	T	1.518e^-5	0.795	INTRON E5	TF binding site mE1_TFBS_cad
3L	16042655	3L_16042655_SNP [dm3] 3L_16049555_SNP [dm6]	T	A	1.527e^-5	0.795	INTRON th & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3L	13135282	3L_13135282_SNP [dm3] 3L_13142182_SNP [dm6]	G	A	1.612e^-5	0.814	INTERGENIC
3L	1078132	3L_1078132_INS [dm3] 3L_1078132_INS [dm6]	A	AAACAATTGAA...	1.766e^-5	0.814	INTRON bab1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	16785902	2L_16785902_SNP [dm3] 2L_16785902_SNP [dm6]	C	A	1.838e^-5	0.814	SPLICE_SITE_REGION Mhc INTRON Mhc	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2L	18996560	2L_18996560_SNP [dm3] 2L_18996560_SNP [dm6]	G	A	1.916e^-5	0.814	UPSTREAM CG10650 & 1 other INTERGENIC
3L	2747058	3L_2747058_SNP [dm3] 3L_2747058_SNP [dm6]	A	G	1.951e^-5	0.814	INTRON Mrtf
3L	953093	3L_953093_SNP [dm3] 3L_953093_SNP [dm6]	T	G	2.148e^-5	0.814	INTRON Glut1
3L	953104	3L_953104_SNP [dm3] 3L_953104_SNP [dm6]	C	T	2.148e^-5	0.814	INTRON Glut1
3L	953115	3L_953115_SNP [dm3] 3L_953115_SNP [dm6]	G	T	2.148e^-5	0.814	INTRON Glut1
2R	9628067	2R_9628067_SNP [dm3] 2R_13740562_SNP [dm6]	A	C	2.186e^-5	0.814	INTRON fas
3R	25614225	3R_25614225_SNP [dm3] 3R_29788503_SNP [dm6]	G	C	2.238e^-5	0.814	UPSTREAM kay INTRON kay
3L	14509408	3L_14509408_SNP [dm3] 3L_14516308_SNP [dm6]	A	T	2.291e^-5	0.814	INTRON bbg
3R	22287887	3R_22287887_SNP [dm3] 3R_26462165_SNP [dm6]	C	G	2.293e^-5	0.814	INTRON CG5455
2L	16785886	2L_16785886_SNP [dm3] 2L_16785886_SNP [dm6]	C	T	2.304e^-5	0.814	INTRON Mhc	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13013924	3L_13013924_SNP [dm3] 3L_13020824_SNP [dm6]	G	A	2.341e^-5	0.814	SPLICE_SITE_REGION AdenoK SYNONYMOUS_CODING AdenoK
3R	8854737	3R_8854737_SNP [dm3] 3R_13029015_SNP [dm6]	G	C	2.347e^-5	0.814	UTR_3_PRIME CG12360 INTRON CG12360
3R	9698667	3R_9698667_SNP [dm3] 3R_13872945_SNP [dm6]	T	C	2.361e^-5	0.814	INTRON E5
3R	9698668	3R_9698668_SNP [dm3] 3R_13872946_SNP [dm6]	C	A	2.361e^-5	0.814	INTRON E5
X	10822100	X_10822100_SNP [dm3] X_10928067_SNP [dm6]	G	T	2.379e^-5	0.814	SYNONYMOUS_CODING CG2145	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3R	18463603	3R_18463603_SNP [dm3] 3R_22637881_SNP [dm6]	G	A	2.388e^-5	0.814	SYNONYMOUS_CODING loco	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	7197367	3L_7197367_DEL [dm3] 3L_7204267_DEL [dm6]	ACACA	A	2.455e^-5	0.822	INTERGENIC
3R	13727864	3R_13727864_SNP [dm3] 3R_17902142_SNP [dm6]	A	C	2.546e^-5	0.832	INTRON Rim
3L	18480378	3L_18480378_SNP [dm3] 3L_18487278_SNP [dm6]	A	C	2.597e^-5	0.832	INTRON AstC-R2
3R	9698686	3R_9698686_SNP [dm3] 3R_13872964_SNP [dm6]	A	T	2.670e^-5	0.832	INTRON E5
3L	7197582	3L_7197582_SNP [dm3] 3L_7204482_SNP [dm6]	G	A	2.797e^-5	0.832	INTERGENIC
2L	7159522	2L_7159522_SNP [dm3] 2L_7159522_SNP [dm6]	G	T	2.850e^-5	0.832	INTERGENIC
3R	13378834	3R_13378834_SNP [dm3] 3R_17553112_SNP [dm6]	G	C	2.897e^-5	0.832	INTERGENIC
3L	13947517	3L_13947517_SNP [dm3] 3L_13954417_SNP [dm6]	C	T	2.903e^-5	0.832	INTRON CG32137
X	10821803	X_10821803_SNP [dm3] X_10927770_SNP [dm6]	A	G	2.941e^-5	0.832	SYNONYMOUS_CODING CG2145	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	15618277	3R_15618277_SNP [dm3] 3R_19792555_SNP [dm6]	A	G	2.979e^-5	0.832	INTERGENIC
X	10835715	X_10835715_SNP [dm3] X_10941682_SNP [dm6]	C	T	3.066e^-5	0.832	INTRON Myo10A	TF binding site mE1_TFBS_chinmo
X	10835719	X_10835719_SNP [dm3] X_10941686_SNP [dm6]	G	C	3.066e^-5	0.832	INTRON Myo10A	TF binding site mE1_TFBS_chinmo
3R	15617394	3R_15617394_SNP [dm3] 3R_19791672_SNP [dm6]	C	T	3.076e^-5	0.832	DOWNSTREAM tRNA:CR31215 INTERGENIC
3L	6801849	3L_6801849_SNP [dm3] 3L_6808749_SNP [dm6]	A	T	3.149e^-5	0.832	INTERGENIC
2L	12146126	2L_12146126_SNP [dm3] 2L_12146126_SNP [dm6]	A	T	3.178e^-5	0.832	INTRON CG31760
2R	19944472	2R_19944472_SNP [dm3] 2R_24056949_SNP [dm6]	C	T	3.189e^-5	0.832	SYNONYMOUS_CODING CG13563 UPSTREAM eIF-5A INTRON ppk29	TF binding site BDTNP1_TFBS_dl mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
2R	11105658	2R_11105658_SNP [dm3] 2R_15218153_SNP [dm6]	T	A	3.219e^-5	0.832	UPSTREAM CG8079 & 1 other DOWNSTREAM Hex-C EXON CR44463	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Ubx mE1_TFBS_zfh1
2R	6950919	2R_6950919_SNP [dm3] 2R_11063414_SNP [dm6]	T	C	3.251e^-5	0.832	INTRON luna	TF binding site BDTNP1_TFBS_twi
X	6024159	X_6024159_SNP [dm3] X_6130126_SNP [dm6]	C	T	3.354e^-5	0.832	INTRON Ca-alpha1T
3R	15617691	3R_15617691_SNP [dm3] 3R_19791969_SNP [dm6]	C	T	3.417e^-5	0.832	DOWNSTREAM tRNA:CR31215 INTERGENIC
3R	25059049	3R_25059049_SNP [dm3] 3R_29233327_SNP [dm6]	T	C	3.440e^-5	0.832	SYNONYMOUS_CODING CG15817	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	9949250	X_9949250_SNP [dm3] X_10055217_SNP [dm6]	T	A	3.488e^-5	0.832	SYNONYMOUS_CODING Yp1 UPSTREAM CR45601 DOWNSTREAM CG15312
2L	6014461	2L_6014461_SNP [dm3] 2L_6014461_SNP [dm6]	G	A	3.526e^-5	0.832	INTRON H2.0
3L	12316808	3L_12316808_SNP [dm3] 3L_12323708_SNP [dm6]	C	G	3.543e^-5	0.832	INTERGENIC
3L	14092590	3L_14092590_DEL [dm3] 3L_14099490_DEL [dm6]	AGATACGATTTTACATTCAA...	A	3.551e^-5	0.832	INTERGENIC
3L	7197138	3L_7197138_SNP [dm3] 3L_7204038_SNP [dm6]	T	C	3.648e^-5	0.844	INTERGENIC
2R	14806763	2R_14806763_SNP [dm3] 2R_18919258_SNP [dm6]	A	T	3.781e^-5	0.853	INTRON sano
X	10822097	X_10822097_SNP [dm3] X_10928064_SNP [dm6]	C	A	3.798e^-5	0.853	SYNONYMOUS_CODING CG2145	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7197096	3L_7197096_SNP [dm3] 3L_7203996_SNP [dm6]	A	G	3.859e^-5	0.853	INTERGENIC
2L	1086102	2L_1086102_SNP [dm3] 2L_1086102_SNP [dm6]	A	G	3.889e^-5	0.853	DOWNSTREAM Atg4a INTRON CG4629	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2R	19227203	2R_19227203_SNP [dm3] 2R_23339680_SNP [dm6]	G	C	4.023e^-5	0.853	INTERGENIC
X	9684409	X_9684409_INS [dm3] X_9790376_INS [dm6]	C	CG	4.037e^-5	0.853	INTRON CG32698	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
X	10821716	X_10821716_SNP [dm3] X_10927683_SNP [dm6]	A	T	4.091e^-5	0.853	INTRON CG2145	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	415069	3L_415069_SNP [dm3] 3L_415069_SNP [dm6]	T	G	4.105e^-5	0.853	INTERGENIC
X	10821731	X_10821731_SNP [dm3] X_10927698_SNP [dm6]	A	G	4.127e^-5	0.853	INTRON CG2145	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	10818970	X_10818970_SNP [dm3] X_10924937_SNP [dm6]	T	C	4.232e^-5	0.853	SYNONYMOUS_CODING v
3R	16748181	3R_16748181_SNP [dm3] 3R_20922459_SNP [dm6]	C	T	4.234e^-5	0.853	INTRON CG31191 & 1 other
2L	5512607	2L_5512607_SNP [dm3] 2L_5512607_SNP [dm6]	C	T	4.253e^-5	0.853	INTERGENIC
2R	10104260	2R_10104260_SNP [dm3] 2R_14216755_SNP [dm6]	G	A	4.361e^-5	0.853	UPSTREAM mir-308 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Ubx
3R	13457777	3R_13457777_SNP [dm3] 3R_17632055_SNP [dm6]	T	C	4.366e^-5	0.853	UPSTREAM tRNA:CR31569 DOWNSTREAM tRNA:CR31573 INTRON CG43175
3L	7520521	3L_7520521_SNP [dm3] 3L_7527421_SNP [dm6]	C	T	4.378e^-5	0.853	UTR_3_PRIME ltl
2L	2596849	2L_2596849_SNP [dm3] 2L_2596849_SNP [dm6]	A	T	4.414e^-5	0.853	INTERGENIC
3R	13457710	3R_13457710_SNP [dm3] 3R_17631988_SNP [dm6]	A	G	4.481e^-5	0.857	UPSTREAM tRNA:CR31569 DOWNSTREAM tRNA:CR31573 INTRON CG43175
3R	18528768	3R_18528768_SNP [dm3] 3R_22703046_SNP [dm6]	C	G	4.543e^-5	0.86	SPLICE_SITE_REGION CG6972 UPSTREAM CCAP INTRON CG6972	TF binding site mE1_TFBS_inv
3L	14509375	3L_14509375_SNP [dm3] 3L_14516275_SNP [dm6]	A	T	4.634e^-5	0.862	INTRON bbg

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

HSC70_4_CT phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results