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=7.951e^-2)
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_3R_Mo	0.02573

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1583 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	20286602	X_20286602_SNP [dm3] X_20415575_SNP [dm6]	G	A	3.107e^-6	0.806	UPSTREAM Obp19a INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	22839348	3L_22839348_SNP [dm3] 3L_22846248_SNP [dm6]	G	C	4.541e^-6	0.806	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	11900713	3R_11900713_SNP [dm3] 3R_16074991_SNP [dm6]	A	T	5.158e^-6	0.806	SYNONYMOUS_CODING Mhcl INTRON Mhcl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11388928	3L_11388928_SNP [dm3] 3L_11395828_SNP [dm6]	A	G	5.952e^-6	0.806	DOWNSTREAM CG11726 INTERGENIC
2R	7266250	2R_7266250_SNP [dm3] 2R_11378745_SNP [dm6]	C	A	6.166e^-6	0.806	INTRON Tsp47F
3L	7449822	3L_7449822_SNP [dm3] 3L_7456722_SNP [dm6]	A	G	7.313e^-6	0.806	SYNONYMOUS_CODING ppk26
3L	7449825	3L_7449825_SNP [dm3] 3L_7456725_SNP [dm6]	C	T	7.313e^-6	0.806	SYNONYMOUS_CODING ppk26
3R	11901121	3R_11901121_SNP [dm3] 3R_16075399_SNP [dm6]	A	G	1.414e^-5	0.806	SYNONYMOUS_CODING Mhcl INTRON Mhcl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	19295226	2L_19295226_SNP [dm3] 2L_19295226_SNP [dm6]	C	T	1.436e^-5	0.806	INTERGENIC
2R	6622403	2R_6622403_SNP [dm3] 2R_10734898_SNP [dm6]	C	T	1.499e^-5	0.806	UPSTREAM CG7220 INTRON CG7220
2R	10454281	2R_10454281_SNP [dm3] 2R_14566776_SNP [dm6]	G	C	1.634e^-5	0.806	INTRON ttv
2L	19295258	2L_19295258_SNP [dm3] 2L_19295258_SNP [dm6]	A	G	1.718e^-5	0.806	INTERGENIC
X	12438864	X_12438864_SNP [dm3] X_12544831_SNP [dm6]	T	A	1.920e^-5	0.806	INTRON CG43921
X	15249142	X_15249142_SNP [dm3] X_15355109_SNP [dm6]	G	C	2.012e^-5	0.806	INTRON acj6
3L	22840382	3L_22840382_SNP [dm3] 3L_22847282_SNP [dm6]	G	T	2.081e^-5	0.806	DOWNSTREAM tRNA:CR32460 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	10138347	3L_10138347_SNP [dm3] 3L_10145247_SNP [dm6]	C	T	2.116e^-5	0.806	INTERGENIC
3L	22836321	3L_22836321_SNP [dm3] 3L_22843221_SNP [dm6]	A	T	2.122e^-5	0.806	UPSTREAM tRNA:CR32456 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	22831215	3L_22831215_SNP [dm3] 3L_22838115_SNP [dm6]	C	A	2.130e^-5	0.806	UTR_3_PRIME CG11226	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3R	6711687	3R_6711687_SNP [dm3] 3R_10885965_SNP [dm6]	C	T	2.300e^-5	0.806	UTR_5_PRIME Leash UPSTREAM CG14696	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	1617410	2L_1617410_DEL [dm3] 2L_1617410_DEL [dm6]	AA	A	2.366e^-5	0.806	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo
3L	19917857	3L_19917857_DEL [dm3] 3L_19924757_DEL [dm6]	TA	G	2.506e^-5	0.806	UPSTREAM Grasp65 DOWNSTREAM CG7770 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	11609712	2L_11609712_SNP [dm3] 2L_11609712_SNP [dm6]	T	C	2.557e^-5	0.806	DOWNSTREAM spag4 INTRON kek2	TF binding site mE1_TFBS_inv
3L	11388971	3L_11388971_INS [dm3] 3L_11395871_INS [dm6]	A	AT	2.611e^-5	0.806	DOWNSTREAM CG11726 INTERGENIC
2L	8503577	2L_8503577_SNP [dm3] 2L_8503577_SNP [dm6]	C	T	2.766e^-5	0.806	INTRON Dh31
2R	10529846	2R_10529846_SNP [dm3] 2R_14642341_SNP [dm6]	T	G	2.788e^-5	0.806	INTERGENIC
2R	10529851	2R_10529851_SNP [dm3] 2R_14642346_SNP [dm6]	A	G	2.788e^-5	0.806	INTERGENIC
X	12336250	X_12336250_SNP [dm3] X_12442217_SNP [dm6]	A	C	2.864e^-5	0.806	INTRON Pkcdelta
X	12336269	X_12336269_SNP [dm3] X_12442236_SNP [dm6]	A	G	2.978e^-5	0.806	INTRON Pkcdelta
3R	6725942	3R_6725942_SNP [dm3] 3R_10900220_SNP [dm6]	A	T	2.982e^-5	0.806	INTERGENIC
3L	7282284	3L_7282284_SNP [dm3] 3L_7289184_SNP [dm6]	T	C	3.097e^-5	0.806	INTRON unc-13-4A
3L	22840909	3L_22840909_SNP [dm3] 3L_22847809_SNP [dm6]	G	C	3.097e^-5	0.806	UPSTREAM tRNA:CR32460 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	22840930	3L_22840930_SNP [dm3] 3L_22847830_SNP [dm6]	G	T	3.097e^-5	0.806	UPSTREAM tRNA:CR32460 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	22847103	3L_22847103_SNP [dm3] 3L_22854003_SNP [dm6]	A	C	3.171e^-5	0.806	UPSTREAM CG32462 DOWNSTREAM CG32459 & 1 other EXON CR43426
3R	6724270	3R_6724270_SNP [dm3] 3R_10898548_SNP [dm6]	C	A	3.283e^-5	0.806	EXON CR45578	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	6721222	3R_6721222_SNP [dm3] 3R_10895500_SNP [dm6]	C	A	3.379e^-5	0.806	UTR_3_PRIME Leash DOWNSTREAM CR45577	TF binding site mE1_TFBS_HSA mE1_TFBS_run
3R	6721449	3R_6721449_SNP [dm3] 3R_10895727_SNP [dm6]	A	T	3.379e^-5	0.806	UTR_3_PRIME Leash DOWNSTREAM CR45577	TF binding site mE1_TFBS_HSA mE1_TFBS_run
X	9095176	X_9095176_SNP [dm3] X_9201143_SNP [dm6]	C	T	3.432e^-5	0.806	INTRON su_r_
X	14748120	X_14748120_SNP [dm3] X_14854087_SNP [dm6]	A	G	3.501e^-5	0.806	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14748327	X_14748327_SNP [dm3] X_14854294_SNP [dm6]	A	T	3.501e^-5	0.806	DOWNSTREAM CG9519 INTRON Flo2
X	14747743	X_14747743_SNP [dm3] X_14853710_SNP [dm6]	A	G	3.527e^-5	0.806	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
3L	14102639	3L_14102639_SNP [dm3] 3L_14109539_SNP [dm6]	C	G	3.537e^-5	0.806	INTERGENIC	TF binding site mE1_TFBS_zfh1
3L	22844112	3L_22844112_SNP [dm3] 3L_22851012_SNP [dm6]	C	T	3.715e^-5	0.806	INTRON CR43426	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
3R	19204995	3R_19204995_SNP [dm3] 3R_23379273_SNP [dm6]	A	G	3.778e^-5	0.806	SYNONYMOUS_CODING CG4393	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	6828122	X_6828122_SNP [dm3] X_6934089_SNP [dm6]	C	G	3.854e^-5	0.806	INTRON CG14431
3R	6722870	3R_6722870_SNP [dm3] 3R_10897148_SNP [dm6]	G	A	3.998e^-5	0.806	DOWNSTREAM Leash & 1 other EXON CR45577	TF binding site BDTNP1_TFBS_sna
3L	11925572	3L_11925572_SNP [dm3] 3L_11932472_SNP [dm6]	T	G	4.152e^-5	0.806	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	15333095	3R_15333095_SNP [dm3] 3R_19507373_SNP [dm6]	T	A	4.248e^-5	0.806	INTRON Dys
X	14748016	X_14748016_SNP [dm3] X_14853983_SNP [dm6]	C	A	4.261e^-5	0.806	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
2L	5462385	2L_5462385_INS [dm3] 2L_5462385_INS [dm6]	T	TCTCGT	4.371e^-5	0.806	INTRON mid	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z
X	8097972	X_8097972_SNP [dm3] X_8203939_SNP [dm6]	G	A	4.442e^-5	0.806	INTRON sdt
3L	12503572	3L_12503572_SNP [dm3] 3L_12510472_SNP [dm6]	A	C	4.462e^-5	0.806	SYNONYMOUS_CODING sti
2L	5459601	2L_5459601_SNP [dm3] 2L_5459601_SNP [dm6]	T	C	4.505e^-5	0.806	INTERGENIC	TF binding site BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	6723020	3R_6723020_SNP [dm3] 3R_10897298_SNP [dm6]	T	G	4.579e^-5	0.806	UPSTREAM CR45577 DOWNSTREAM Leash & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_sna
3R	6723042	3R_6723042_SNP [dm3] 3R_10897320_SNP [dm6]	T	G	4.579e^-5	0.806	UPSTREAM CR45577 DOWNSTREAM Leash & 1 other INTERGENIC
3R	6723062	3R_6723062_SNP [dm3] 3R_10897340_SNP [dm6]	A	T	4.579e^-5	0.806	UPSTREAM CR45577 DOWNSTREAM Leash & 1 other INTERGENIC
3R	6723105	3R_6723105_SNP [dm3] 3R_10897383_SNP [dm6]	G	A	4.579e^-5	0.806	UPSTREAM CR45577 DOWNSTREAM Leash & 1 other INTERGENIC
3R	6723117	3R_6723117_SNP [dm3] 3R_10897395_SNP [dm6]	C	A	4.579e^-5	0.806	UPSTREAM CR45577 DOWNSTREAM Leash & 1 other INTERGENIC
3R	6723422	3R_6723422_SNP [dm3] 3R_10897700_SNP [dm6]	G	C	4.579e^-5	0.806	UPSTREAM CR45577 DOWNSTREAM CR45578 INTERGENIC
3R	6725863	3R_6725863_SNP [dm3] 3R_10900141_SNP [dm6]	A	T	4.579e^-5	0.806	INTERGENIC
3R	6728775	3R_6728775_SNP [dm3] 3R_10903053_SNP [dm6]	C	T	4.579e^-5	0.806	INTERGENIC
3R	6734973	3R_6734973_SNP [dm3] 3R_10909251_SNP [dm6]	G	A	4.579e^-5	0.806	INTERGENIC
3R	6735382	3R_6735382_SNP [dm3] 3R_10909660_SNP [dm6]	C	A	4.579e^-5	0.806	INTERGENIC
3R	19655670	3R_19655670_SNP [dm3] 3R_23829948_SNP [dm6]	C	T	4.793e^-5	0.806	INTRON CG34355
X	9929877	X_9929877_SNP [dm3] X_10035844_SNP [dm6]	A	G	4.795e^-5	0.806	SYNONYMOUS_CODING Cht6 INTRON Cht6	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	12336300	X_12336300_SNP [dm3] X_12442267_SNP [dm6]	A	T	4.802e^-5	0.806	INTRON Pkcdelta
3R	6736381	3R_6736381_SNP [dm3] 3R_10910659_SNP [dm6]	T	C	4.840e^-5	0.806	INTERGENIC
X	17181219	X_17181219_SNP [dm3] X_17287186_SNP [dm6]	G	A	4.980e^-5	0.806	SYNONYMOUS_CODING Fim INTRON CG5445	TF binding site mE1_TFBS_HSA
3R	6791097	3R_6791097_SNP [dm3] 3R_10965375_SNP [dm6]	A	G	5.065e^-5	0.806	INTERGENIC
2R	7266275	2R_7266275_SNP [dm3] 2R_11378770_SNP [dm6]	T	G	5.195e^-5	0.806	INTRON Tsp47F
3L	778267	3L_778267_SNP [dm3] 3L_778267_SNP [dm6]	C	T	5.257e^-5	0.806	INTERGENIC
3L	421598	3L_421598_SNP [dm3] 3L_421598_SNP [dm6]	T	C	5.325e^-5	0.806	INTERGENIC	TF binding site mE1_TFBS_sens
3L	22839638	3L_22839638_SNP [dm3] 3L_22846538_SNP [dm6]	G	C	5.350e^-5	0.806	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	20377587	3R_20377587_SNP [dm3] 3R_24551865_SNP [dm6]	T	C	5.492e^-5	0.806	INTRON Esyt2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	24200726	3R_24200726_SNP [dm3] 3R_28375004_SNP [dm6]	G	A	5.530e^-5	0.806	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8177294	2R_8177294_SNP [dm3] 2R_12289789_SNP [dm6]	T	C	5.668e^-5	0.806	UPSTREAM CG42700 INTRON CG42700
2R	8177295	2R_8177295_SNP [dm3] 2R_12289790_SNP [dm6]	T	C	5.668e^-5	0.806	UPSTREAM CG42700 INTRON CG42700
2R	6213515	2R_6213515_INS [dm3] 2R_10326010_INS [dm6]	T	TGT	5.706e^-5	0.806	INTRON CG42732
3L	11925809	3L_11925809_SNP [dm3] 3L_11932709_SNP [dm6]	A	G	5.809e^-5	0.806	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	14170739	2R_14170739_SNP [dm3] 2R_18283234_SNP [dm6]	A	G	5.853e^-5	0.806	SYNONYMOUS_CODING sbb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	14170753	2R_14170753_SNP [dm3] 2R_18283248_SNP [dm6]	A	C	5.853e^-5	0.806	SPLICE_SITE_REGION sbb INTRON sbb	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11937635	3L_11937635_SNP [dm3] 3L_11944535_SNP [dm6]	G	A	5.929e^-5	0.806	SYNONYMOUS_CODING CG5883
3L	5910770	3L_5910770_SNP [dm3] 3L_5917670_SNP [dm6]	C	A	5.989e^-5	0.806	UPSTREAM CR45167 DOWNSTREAM CG10483 & 1 other INTERGENIC
X	12336260	X_12336260_SNP [dm3] X_12442227_SNP [dm6]	A	C	6.204e^-5	0.806	INTRON Pkcdelta
3R	17947127	3R_17947127_SNP [dm3] 3R_22121405_SNP [dm6]	C	G	6.227e^-5	0.806	INTRON CG42390
3L	4064248	3L_4064248_SNP [dm3] 3L_4064248_SNP [dm6]	A	T	6.267e^-5	0.806	UTR_3_PRIME dib & 1 other	TF binding site mE1_TFBS_cad
2R	8177177	2R_8177177_SNP [dm3] 2R_12289672_SNP [dm6]	A	G	6.275e^-5	0.806	INTRON CG42700
X	9095198	X_9095198_DEL [dm3] X_9201165_DEL [dm6]	TGTGAATAGCCATAACTATT...	T	6.281e^-5	0.806	INTRON su_r_
X	19399201	X_19399201_SNP [dm3] X_19505168_SNP [dm6]	A	G	6.401e^-5	0.806	UPSTREAM Pfrx INTRON Pfrx & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
X	14748166	X_14748166_SNP [dm3] X_14854133_SNP [dm6]	G	T	6.468e^-5	0.806	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14748179	X_14748179_SNP [dm3] X_14854146_SNP [dm6]	A	T	6.468e^-5	0.806	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
X	14748180	X_14748180_SNP [dm3] X_14854147_SNP [dm6]	C	T	6.468e^-5	0.806	UPSTREAM CG9521 DOWNSTREAM CG9519 INTRON Flo2
2R	4071675	2R_4071675_SNP [dm3] 2R_8184170_SNP [dm6]	G	A	6.543e^-5	0.806	INTRON LRP1
X	2908434	X_2908434_SNP [dm3] X_3014401_SNP [dm6]	G	A	6.550e^-5	0.806	INTRON kirre
X	12336171	X_12336171_DEL [dm3] X_12442138_DEL [dm6]	TAGTATGTTACAAAGAATTC...	T	6.617e^-5	0.806	INTRON Pkcdelta
3L	11359686	3L_11359686_SNP [dm3] 3L_11366586_SNP [dm6]	T	G	6.623e^-5	0.806	DOWNSTREAM CR45036 INTERGENIC	TF binding site mE1_TFBS_inv
3L	3955833	3L_3955833_SNP [dm3] 3L_3955833_SNP [dm6]	T	C	6.688e^-5	0.806	UTR_3_PRIME CG12605
2R	15477633	2R_15477633_DEL [dm3] 2R_19590128_DEL [dm6]	TT	T	6.717e^-5	0.806	INTRON sm
3L	10194208	3L_10194208_SNP [dm3] 3L_10201108_SNP [dm6]	T	A	7.112e^-5	0.806	INTRON ect
3R	6735381	3R_6735381_SNP [dm3] 3R_10909659_SNP [dm6]	T	C	7.228e^-5	0.806	INTERGENIC
X	5483492	X_5483492_SNP [dm3] X_5589459_SNP [dm6]	G	A	7.230e^-5	0.806	INTERGENIC	TF binding site mE1_TFBS_inv

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

sons2 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results