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=1.820e^-2)
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	0.03115
In_2L_t	0.01041
In_2R_NS	0.02188

Kruskal-Wallis test

Covariate	χ²	p-value
wolba	3.3586	0.0669
In_2L_t	7.2257	0.027
In_2R_NS	6.1453	0.0463

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2089 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
X	10855844	X_10855844_SNP [dm3] X_10961811_SNP [dm6]	G	A	6.600e^-7	0.693	INTRON Myo10A
3L	16532066	3L_16532066_DEL [dm3] 3L_16538966_DEL [dm6]	CA	C	1.178e^-6	0.693	INTRON CG43373
2L	7958966	2L_7958966_SNP [dm3] 2L_7958966_SNP [dm6]	G	T	2.507e^-6	0.693	INTRON Snoo
2R	15248610	2R_15248610_SNP [dm3] 2R_19361105_SNP [dm6]	A	C	2.547e^-6	0.693	SYNONYMOUS_CODING CG11961
2R	15248616	2R_15248616_SNP [dm3] 2R_19361111_SNP [dm6]	T	C	2.547e^-6	0.693	SYNONYMOUS_CODING CG11961
3L	16532158	3L_16532158_SNP [dm3] 3L_16539058_SNP [dm6]	C	G	2.837e^-6	0.693	INTRON CG43373
2R	17397098	2R_17397098_SNP [dm3] 2R_21509593_SNP [dm6]	G	T	2.921e^-6	0.693	INTRON MESK2
2L	9405390	2L_9405390_SNP [dm3] 2L_9405390_SNP [dm6]	G	A	2.956e^-6	0.693	INTRON Shawl
2L	12516588	2L_12516588_SNP [dm3] 2L_12516588_SNP [dm6]	A	G	4.283e^-6	0.768	SYNONYMOUS_CODING bun INTRON bun	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	6975347	2R_6975347_INS [dm3] 2R_11087842_INS [dm6]	T	TCGTCTAGGTT...	4.572e^-6	0.768	UPSTREAM CG43189 INTRON luna & 1 other	TF binding site mE1_TFBS_Kr
2L	10601264	2L_10601264_SNP [dm3] 2L_10601264_SNP [dm6]	T	C	5.557e^-6	0.768	INTRON Trim9
3L	8949995	3L_8949995_SNP [dm3] 3L_8956895_SNP [dm6]	T	A	5.738e^-6	0.768	DOWNSTREAM GNBP3 INTRON mRpL12	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	16114803	2R_16114803_SNP [dm3] 2R_20227298_SNP [dm6]	A	G	5.857e^-6	0.768	INTERGENIC
2R	15213498	2R_15213498_SNP [dm3] 2R_19325993_SNP [dm6]	C	G	5.903e^-6	0.768	SYNONYMOUS_CODING Rgk1 UPSTREAM Rgk1	TF binding site mE1_TFBS_chinmo mE1_TFBS_Trl
2R	12786317	2R_12786317_SNP [dm3] 2R_16898812_SNP [dm6]	A	G	6.145e^-6	0.768	SYNONYMOUS_CODING inaC
2L	7781627	2L_7781627_SNP [dm3] 2L_7781627_SNP [dm6]	G	A	7.404e^-6	0.86	UTR_5_PRIME CG7164 DOWNSTREAM Uro	TF binding site mE1_TFBS_cad
3R	15642854	3R_15642854_SNP [dm3] 3R_19817132_SNP [dm6]	A	T	8.428e^-6	0.86	INTRON bnl	TF binding site BDTNP1_TFBS_twi
3L	7231135	3L_7231135_SNP [dm3] 3L_7238035_SNP [dm6]	A	T	8.716e^-6	0.86	NON_SYNONYMOUS_CODING CG14829 UPSTREAM BHD	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	10601307	2L_10601307_SNP [dm3] 2L_10601307_SNP [dm6]	T	G	8.960e^-6	0.86	INTRON Trim9
2R	18038355	2R_18038355_INS [dm3] 2R_22150850_INS [dm6]	A	ATA	9.659e^-6	0.86	INTRON a
X	19887748	X_19887748_SNP [dm3] X_19993715_SNP [dm6]	A	G	1.061e^-5	0.86	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	16114766	2R_16114766_SNP [dm3] 2R_20227261_SNP [dm6]	G	T	1.078e^-5	0.86	INTERGENIC
2R	19793574	2R_19793574_SNP [dm3] 2R_23906051_SNP [dm6]	C	T	1.087e^-5	0.86	DOWNSTREAM CG13562 INTRON Nap1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_jumu mE1_TFBS_sens
3R	16165961	3R_16165961_SNP [dm3] 3R_20340239_SNP [dm6]	G	A	1.109e^-5	0.86	NON_SYNONYMOUS_CODING Ir92a
3L	5495045	3L_5495045_SNP [dm3] 3L_5501945_SNP [dm6]	G	A	1.146e^-5	0.86	UPSTREAM CR44519 INTERGENIC
X	19887739	X_19887739_SNP [dm3] X_19993706_SNP [dm6]	G	A	1.198e^-5	0.864	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	7402798	2R_7402798_SNP [dm3] 2R_11515293_SNP [dm6]	A	T	1.390e^-5	0.873	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	11158255	2L_11158255_SNP [dm3] 2L_11158255_SNP [dm6]	G	A	1.494e^-5	0.873	UTR_3_PRIME Ca-beta DOWNSTREAM Ca-beta
3L	16282719	3L_16282719_SNP [dm3] 3L_16289619_SNP [dm6]	T	G	1.570e^-5	0.873	DOWNSTREAM CG13045 INTERGENIC
3L	2744793	3L_2744793_SNP [dm3] 3L_2744793_SNP [dm6]	C	T	1.733e^-5	0.873	INTRON Mrtf
3L	7231158	3L_7231158_SNP [dm3] 3L_7238058_SNP [dm6]	T	C	1.774e^-5	0.873	SYNONYMOUS_CODING CG14829 UPSTREAM BHD	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	11018344	3R_11018344_SNP [dm3] 3R_15192622_SNP [dm6]	T	G	1.792e^-5	0.873	SYNONYMOUS_CODING CG6752 UPSTREAM mir-3644
3R	16165997	3R_16165997_SNP [dm3] 3R_20340275_SNP [dm6]	G	A	1.944e^-5	0.873	NON_SYNONYMOUS_CODING Ir92a
3L	18104074	3L_18104074_SNP [dm3] 3L_18110974_SNP [dm6]	A	G	1.995e^-5	0.873	SYNONYMOUS_CODING mus304	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	18590013	3R_18590013_SNP [dm3] 3R_22764291_SNP [dm6]	A	C	2.075e^-5	0.873	SYNONYMOUS_CODING CG4721 UPSTREAM CG4723 INTRON Usp12-46 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	9803224	X_9803224_DEL [dm3] X_9909191_DEL [dm6]	ATCTTAAGTA	A	2.078e^-5	0.873	UTR_3_PRIME CG1986 DOWNSTREAM CG1986	insulator Insulator_Class_II.mE01
2R	17378918	2R_17378918_SNP [dm3] 2R_21491413_SNP [dm6]	T	G	2.169e^-5	0.873	INTRON Fkbp14
3R	16166844	3R_16166844_SNP [dm3] 3R_20341122_SNP [dm6]	G	A	2.201e^-5	0.873	INTRON Ir92a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	16532177	3L_16532177_SNP [dm3] 3L_16539077_SNP [dm6]	C	A	2.215e^-5	0.873	INTRON CG43373
3R	19037162	3R_19037162_SNP [dm3] 3R_23211440_SNP [dm6]	G	T	2.261e^-5	0.873	INTRON cnc	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
X	10855888	X_10855888_SNP [dm3] X_10961855_SNP [dm6]	A	T	2.301e^-5	0.873	INTRON Myo10A
2R	16175836	2R_16175836_SNP [dm3] 2R_20288331_SNP [dm6]	T	G	2.461e^-5	0.873	UTR_3_PRIME CG34199 DOWNSTREAM Cpr56F
2R	12680355	2R_12680355_SNP [dm3] 2R_16792850_SNP [dm6]	T	A	2.469e^-5	0.873	DOWNSTREAM CG15615 & 1 other INTRON CG15919
2L	16628423	2L_16628423_SNP [dm3] 2L_16628423_SNP [dm6]	T	C	2.583e^-5	0.873	DOWNSTREAM CR44151 INTRON CG42389	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	16304273	2R_16304273_SNP [dm3] 2R_20416768_SNP [dm6]	C	A	2.593e^-5	0.873	INTERGENIC
3R	25974169	3R_25974169_SNP [dm3] 3R_30148447_SNP [dm6]	G	T	2.766e^-5	0.873	INTRON AdoR
3L	4074310	3L_4074310_SNP [dm3] 3L_4074310_SNP [dm6]	T	C	2.774e^-5	0.873	UTR_3_PRIME Gad1 UPSTREAM Faa
X	13964945	X_13964945_INS [dm3] X_14070912_INS [dm6]	A	AA	2.786e^-5	0.873	DOWNSTREAM tRNA:S474:12Eh INTERGENIC
3R	16166816	3R_16166816_SNP [dm3] 3R_20341094_SNP [dm6]	T	C	2.852e^-5	0.873	INTRON Ir92a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	3222769	2L_3222769_SNP [dm3] 2L_3222769_SNP [dm6]	T	A	2.865e^-5	0.873	INTERGENIC
X	20159392	X_20159392_DEL [dm3] X_20288365_DEL [dm6]	ACCTCCAAGAA...	A	2.934e^-5	0.873	INTERGENIC
3R	16165980	3R_16165980_SNP [dm3] 3R_20340258_SNP [dm6]	T	C	2.952e^-5	0.873	SYNONYMOUS_CODING Ir92a
X	14614898	X_14614898_SNP [dm3] X_14720865_SNP [dm6]	T	G	2.980e^-5	0.873	INTRON NetB
2R	3529348	2R_3529348_SNP [dm3] 2R_7641843_SNP [dm6]	A	G	2.998e^-5	0.873	NON_SYNONYMOUS_CODING CG43340 INTRON CG43340	TF binding site mE1_TFBS_cad
3L	1363811	3L_1363811_INS [dm3] 3L_1363811_INS [dm6]	C	CT	3.189e^-5	0.873	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2R	17685083	2R_17685083_DEL [dm3] 2R_21797578_DEL [dm6]	GTC	G	3.192e^-5	0.873	DOWNSTREAM CG34204 & 1 other INTERGENIC
3R	10807767	3R_10807767_SNP [dm3] 3R_14982045_SNP [dm6]	G	A	3.202e^-5	0.873	INTERGENIC
2R	18452463	2R_18452463_SNP [dm3] 2R_22564958_SNP [dm6]	C	T	3.204e^-5	0.873	SYNONYMOUS_CODING dnr1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10686264	2L_10686264_SNP [dm3] 2L_10686264_SNP [dm6]	T	C	3.218e^-5	0.873	UTR_3_PRIME CG7296 DOWNSTREAM CG7296	TF binding site mE1_TFBS_zfh1
X	17276858	X_17276858_SNP [dm3] X_17382825_SNP [dm6]	C	G	3.364e^-5	0.873	INTERGENIC
3R	24418101	3R_24418101_SNP [dm3] 3R_28592379_SNP [dm6]	G	A	3.394e^-5	0.873	DOWNSTREAM MRE23 INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cnc
X	9803405	X_9803405_SNP [dm3] X_9909372_SNP [dm6]	C	T	3.438e^-5	0.873	UTR_3_PRIME CG1986 DOWNSTREAM CG1986
X	20159376	X_20159376_DEL [dm3] X_20288349_DEL [dm6]	AAAAAGACAAAGG...	A	3.491e^-5	0.873	INTERGENIC
2R	17476886	2R_17476886_SNP [dm3] 2R_21589381_SNP [dm6]	G	T	3.640e^-5	0.873	UPSTREAM CG33225 INTERGENIC
2L	10347713	2L_10347713_SNP [dm3] 2L_10347713_SNP [dm6]	A	C	3.719e^-5	0.873	DOWNSTREAM CG34367 & 1 other INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	16114768	2R_16114768_SNP [dm3] 2R_20227263_SNP [dm6]	G	A	3.823e^-5	0.873	INTERGENIC
2R	17924105	2R_17924105_SNP [dm3] 2R_22036600_SNP [dm6]	A	C	3.829e^-5	0.873	DOWNSTREAM CG9308 INTRON CG34370
2R	18182229	2R_18182229_SNP [dm3] 2R_22294724_SNP [dm6]	T	G	3.886e^-5	0.873	SYNONYMOUS_CODING CG5819	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	10503744	2L_10503744_SNP [dm3] 2L_10503744_SNP [dm6]	A	G	3.935e^-5	0.873	INTRON Myo31DF
X	8578764	X_8578764_INS [dm3] X_8684731_INS [dm6]	T	TC	3.977e^-5	0.873	UPSTREAM CG11284 INTRON CG11284
2L	8331177	2L_8331177_SNP [dm3] 2L_8331177_SNP [dm6]	G	A	4.025e^-5	0.873	INTRON CG14275
2L	2439054	2L_2439054_SNP [dm3] 2L_2439054_SNP [dm6]	A	T	4.096e^-5	0.873	INTRON dpp	regulatory region REDfly_CRMs
2L	4055620	2L_4055620_SNP [dm3] 2L_4055620_SNP [dm6]	A	C	4.222e^-5	0.873	INTRON ed	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
2R	15248685	2R_15248685_SNP [dm3] 2R_19361180_SNP [dm6]	C	G	4.231e^-5	0.873	SYNONYMOUS_CODING CG11961
2R	12680354	2R_12680354_SNP [dm3] 2R_16792849_SNP [dm6]	C	T	4.263e^-5	0.873	DOWNSTREAM CG15615 & 1 other INTRON CG15919
2L	16615307	2L_16615307_SNP [dm3] 2L_16615307_SNP [dm6]	T	A	4.326e^-5	0.873	INTRON CG42389
X	10256595	X_10256595_DEL [dm3] X_10362562_DEL [dm6]	TTCTT	T	4.347e^-5	0.873	INTRON l_1_G0289	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_zfh1
3L	10277243	3L_10277243_SNP [dm3] 3L_10284143_SNP [dm6]	C	T	4.378e^-5	0.873	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3R	8701835	3R_8701835_SNP [dm3] 3R_12876113_SNP [dm6]	C	G	4.383e^-5	0.873	INTERGENIC
2R	13496606	2R_13496606_SNP [dm3] 2R_17609101_SNP [dm6]	G	T	4.396e^-5	0.873	NON_SYNONYMOUS_CODING CG10936
2L	16615338	2L_16615338_SNP [dm3] 2L_16615338_SNP [dm6]	A	T	4.477e^-5	0.873	INTRON CG42389
2R	18439537	2R_18439537_SNP [dm3] 2R_22552032_SNP [dm6]	A	T	4.519e^-5	0.873	UTR_3_PRIME CG6018 INTRON px	TF binding site mE1_TFBS_cad
X	3145196	X_3145196_SNP [dm3] X_3251163_SNP [dm6]	A	G	4.758e^-5	0.873	DOWNSTREAM Sgs4 INTRON dnc
X	21280250	X_21280250_SNP [dm3] X_21409223_SNP [dm6]	T	C	4.815e^-5	0.873	DOWNSTREAM CR45003 INTERGENIC
2L	4296683	2L_4296683_SNP [dm3] 2L_4296683_SNP [dm6]	G	T	4.862e^-5	0.873	INTRON tutl
X	16772051	X_16772051_SNP [dm3] X_16878018_SNP [dm6]	G	A	4.907e^-5	0.873	INTERGENIC
2R	15213519	2R_15213519_SNP [dm3] 2R_19326014_SNP [dm6]	G	T	4.953e^-5	0.873	SYNONYMOUS_CODING Rgk1 UPSTREAM Rgk1	TF binding site mE1_TFBS_chinmo mE1_TFBS_Trl
2L	13980790	2L_13980790_SNP [dm3] 2L_13980790_SNP [dm6]	T	G	4.956e^-5	0.873	SYNONYMOUS_CODING NimC2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_cad
2R	15213287	2R_15213287_SNP [dm3] 2R_19325782_SNP [dm6]	C	A	5.056e^-5	0.873	UPSTREAM Rgk1 INTRON Rgk1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	17358439	3R_17358439_SNP [dm3] 3R_21532717_SNP [dm6]	T	C	5.158e^-5	0.873	EXON CR43372
X	16700589	X_16700589_SNP [dm3] X_16806556_SNP [dm6]	A	G	5.213e^-5	0.873	DOWNSTREAM CG13005 INTRON ppk28 & 1 other
2L	10288522	2L_10288522_SNP [dm3] 2L_10288522_SNP [dm6]	A	C	5.279e^-5	0.873	INTRON CG5604
2L	10980755	2L_10980755_SNP [dm3] 2L_10980755_SNP [dm6]	G	A	5.405e^-5	0.873	SYNONYMOUS_CODING SCAR	TF binding site mE1_TFBS_cad
X	16937006	X_16937006_SNP [dm3] X_17042973_SNP [dm6]	C	T	5.472e^-5	0.873	INTRON CG45002
X	9203759	X_9203759_INS [dm3] X_9309726_INS [dm6]	T	TCGTTTCCCTCCCTGA...	5.532e^-5	0.873	INTERGENIC
3L	1710777	3L_1710777_SNP [dm3] 3L_1710777_SNP [dm6]	G	T	5.611e^-5	0.873	INTRON CG7991	TF binding site mE1_TFBS_chinmo
3R	17358561	3R_17358561_SNP [dm3] 3R_21532839_SNP [dm6]	C	A	5.618e^-5	0.873	INTRON CR43372
3R	10807234	3R_10807234_SNP [dm3] 3R_14981512_SNP [dm6]	C	G	5.800e^-5	0.873	INTERGENIC
3L	11628460	3L_11628460_SNP [dm3] 3L_11635360_SNP [dm6]	T	A	5.850e^-5	0.873	INTRON CG32091
X	14614886	X_14614886_SNP [dm3] X_14720853_SNP [dm6]	G	A	5.968e^-5	0.873	INTRON NetB

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

pc_Surv_PRettgeri phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results