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=2.127e^-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_3R_K	0.0317

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	6.7095	0.0349

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1598 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	11359857	3L_11359857_SNP [dm3] 3L_11366757_SNP [dm6]	T	C	6.442e^-7	1	DOWNSTREAM CR45036 INTERGENIC	TF binding site mE1_TFBS_inv
2R	14583678	2R_14583678_SNP [dm3] 2R_18696173_SNP [dm6]	G	A	1.527e^-6	1	UPSTREAM CG15071 INTRON Sik3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18810814	3L_18810814_SNP [dm3] 3L_18817714_SNP [dm6]	T	C	2.161e^-6	1	INTRON CG14073
2L	10592611	2L_10592611_SNP [dm3] 2L_10592611_SNP [dm6]	A	T	2.899e^-6	1	INTRON Trim9
3L	5319539	3L_5319539_SNP [dm3] 3L_5326439_SNP [dm6]	G	A	3.394e^-6	1	INTERGENIC
3R	19154475	3R_19154475_DEL [dm3] 3R_23328753_DEL [dm6]	CACCAGTTGCAGCCACACAA...	C	5.434e^-6	1	INTRON pnt
2R	19425848	2R_19425848_SNP [dm3] 2R_23538325_SNP [dm6]	C	T	5.800e^-6	1	UTR_5_PRIME bw DOWNSTREAM ppk3	TF binding site mE1_TFBS_chinmo
2R	15816475	2R_15816475_SNP [dm3] 2R_19928970_SNP [dm6]	G	A	8.428e^-6	1	INTERGENIC
2R	3293013	2R_3293013_SNP [dm3] 2R_7405508_SNP [dm6]	C	T	9.304e^-6	1	INTRON Eaf
2L	9052204	2L_9052204_SNP [dm3] 2L_9052204_SNP [dm6]	C	T	9.681e^-6	1	UTR_3_PRIME CG31708
2R	19426025	2R_19426025_SNP [dm3] 2R_23538502_SNP [dm6]	C	T	9.696e^-6	1	UPSTREAM bw DOWNSTREAM ppk3 INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	19426028	2R_19426028_SNP [dm3] 2R_23538505_SNP [dm6]	A	T	1.009e^-5	1	UPSTREAM bw DOWNSTREAM ppk3 INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	10848534	2L_10848534_SNP [dm3] 2L_10848534_SNP [dm6]	T	A	1.066e^-5	1	INTRON porin
3R	19775799	3R_19775799_SNP [dm3] 3R_23950077_SNP [dm6]	T	C	1.088e^-5	1	INTERGENIC
2L	16114106	2L_16114106_SNP [dm3] 2L_16114106_SNP [dm6]	G	A	1.148e^-5	1	INTERGENIC
4	764114	4_764114_SNP [dm3] 4_743488_SNP [dm6]	C	T	1.301e^-5	1	INTRON bt
2R	4495165	2R_4495165_SNP [dm3] 2R_8607660_SNP [dm6]	T	G	1.353e^-5	1	INTRON rgr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	4495164	2R_4495164_SNP [dm3] 2R_8607659_SNP [dm6]	T	G	1.489e^-5	1	INTRON rgr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	15625572	3L_15625572_SNP [dm3] 3L_15632472_SNP [dm6]	T	G	1.594e^-5	1	UTR_5_PRIME comm3 INTRON comm3
3R	21833484	3R_21833484_SNP [dm3] 3R_26007762_SNP [dm6]	A	G	1.811e^-5	1	UPSTREAM CR45039 INTERGENIC
3R	19776078	3R_19776078_DEL [dm3] 3R_23950356_DEL [dm6]	TA	T	2.123e^-5	1	INTERGENIC
2R	11173503	2R_11173503_SNP [dm3] 2R_15285998_SNP [dm6]	T	C	2.300e^-5	1	INTRON Trpm	TF binding site mE1_TFBS_chinmo
3L	12487143	3L_12487143_SNP [dm3] 3L_12494043_SNP [dm6]	T	G	2.396e^-5	1	DOWNSTREAM CR45682 INTRON CG10657	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2R	19370364	2R_19370364_SNP [dm3] 2R_23482841_SNP [dm6]	C	T	2.415e^-5	1	INTRON CG43795
3R	25562159	3R_25562159_SNP [dm3] 3R_29736437_SNP [dm6]	C	T	2.422e^-5	1	SPLICE_SITE_REGION CG7601 UPSTREAM CG7598 INTRON CG7601	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens mE1_TFBS_Ubx
3L	1966180	3L_1966180_SNP [dm3] 3L_1966180_SNP [dm6]	G	A	2.457e^-5	1	SYNONYMOUS_CODING SCOT DOWNSTREAM CG1927	TF binding site mE1_TFBS_chinmo
3L	7936243	3L_7936243_SNP [dm3] 3L_7943143_SNP [dm6]	A	T	2.582e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad
3L	5320154	3L_5320154_SNP [dm3] 3L_5327054_SNP [dm6]	A	G	2.590e^-5	1	INTERGENIC
2L	16114337	2L_16114337_SNP [dm3] 2L_16114337_SNP [dm6]	G	A	2.643e^-5	1	INTERGENIC
3L	8807600	3L_8807600_SNP [dm3] 3L_8814500_SNP [dm6]	C	T	2.666e^-5	1	INTERGENIC
3L	9583078	3L_9583078_SNP [dm3] 3L_9589978_SNP [dm6]	T	G	2.706e^-5	1	INTRON CG42673
3L	18138249	3L_18138249_SNP [dm3] 3L_18145149_SNP [dm6]	C	T	2.740e^-5	1	UTR_3_PRIME gk
3R	13756841	3R_13756841_INS [dm3] 3R_17931119_INS [dm6]	A	ATTCACCATC	2.844e^-5	1	UPSTREAM cpo INTRON cpo
3L	14162655	3L_14162655_SNP [dm3] 3L_14169555_SNP [dm6]	G	A	2.871e^-5	1	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	18002783	3R_18002783_SNP [dm3] 3R_22177061_SNP [dm6]	G	A	2.909e^-5	1	INTRON SKIP
2R	7766277	2R_7766277_SNP [dm3] 2R_11878772_SNP [dm6]	A	T	3.025e^-5	1	NON_SYNONYMOUS_CODING CG13185
3R	19034124	3R_19034124_SNP [dm3] 3R_23208402_SNP [dm6]	G	C	3.056e^-5	1	INTRON cnc
X	3518233	X_3518233_SNP [dm3] X_3624200_SNP [dm6]	G	A	3.097e^-5	1	INTRON AstA-R1
3R	12424458	3R_12424458_SNP [dm3] 3R_16598736_SNP [dm6]	T	G	3.176e^-5	1	SYNONYMOUS_CODING CG10345
X	5027960	X_5027960_SNP [dm3] X_5133927_SNP [dm6]	A	T	3.271e^-5	1	DOWNSTREAM Rpn13R INTRON rg & 1 other
3L	19343014	3L_19343014_SNP [dm3] 3L_19349914_SNP [dm6]	T	G	3.273e^-5	1	INTRON CG32206
2L	12725277	2L_12725277_SNP [dm3] 2L_12725277_SNP [dm6]	C	T	3.312e^-5	1	INTRON MRP
4	759124	4_759124_SNP [dm3] 4_738498_SNP [dm6]	A	G	3.366e^-5	1	INTRON bt
3R	12424401	3R_12424401_SNP [dm3] 3R_16598679_SNP [dm6]	C	A	3.366e^-5	1	SYNONYMOUS_CODING CG10345
3R	12424461	3R_12424461_SNP [dm3] 3R_16598739_SNP [dm6]	T	G	3.366e^-5	1	SYNONYMOUS_CODING CG10345
2L	1632386	2L_1632386_SNP [dm3] 2L_1632386_SNP [dm6]	A	T	3.376e^-5	1	INTERGENIC
X	4416329	X_4416329_SNP [dm3] X_4522296_SNP [dm6]	G	T	3.512e^-5	1	INTRON CR32773
X	4772869	X_4772869_SNP [dm3] X_4878836_SNP [dm6]	G	C	3.540e^-5	1	INTRON CG42594
3L	5748434	3L_5748434_SNP [dm3] 3L_5755334_SNP [dm6]	G	T	3.639e^-5	1	INTRON Ubp64E
2L	12725430	2L_12725430_SNP [dm3] 2L_12725430_SNP [dm6]	G	T	3.740e^-5	1	INTRON MRP
2L	920954	2L_920954_SNP [dm3] 2L_920954_SNP [dm6]	T	G	3.803e^-5	1	INTERGENIC
3L	710315	3L_710315_SNP [dm3] 3L_710315_SNP [dm6]	G	A	3.964e^-5	1	NON_SYNONYMOUS_CODING CkIIalpha-i3 UTR_5_PRIME CkIIalpha-i3 DOWNSTREAM CG13896	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA
2R	3292947	2R_3292947_SNP [dm3] 2R_7405442_SNP [dm6]	G	A	4.037e^-5	1	INTRON Eaf
3L	7897796	3L_7897796_SNP [dm3] 3L_7904696_SNP [dm6]	T	A	4.064e^-5	1	INTRON pbl
4	201055	4_201055_SNP [dm3] 4_180429_SNP [dm6]	G	T	4.148e^-5	1	INTERGENIC	transposable element FlyBase
3R	19071977	3R_19071977_SNP [dm3] 3R_23246255_SNP [dm6]	G	A	4.172e^-5	1	INTRON CG4467
3L	22890307	3L_22890307_SNP [dm3] 3L_22897207_SNP [dm6]	A	C	4.299e^-5	1	DOWNSTREAM CR44688 & 1 other INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	3260622	2L_3260622_SNP [dm3] 2L_3260622_SNP [dm6]	C	T	4.377e^-5	1	DOWNSTREAM CR45337 INTERGENIC
4	316731	4_316731_SNP [dm3] 4_296105_SNP [dm6]	C	A	4.459e^-5	1	INTRON Syt7	transposable element FlyBase
2R	8579498	2R_8579498_SNP [dm3] 2R_12691993_SNP [dm6]	A	G	4.476e^-5	1	SYNONYMOUS_CODING CG8768	TF binding site mE1_TFBS_sens
3L	5320475	3L_5320475_SNP [dm3] 3L_5327375_SNP [dm6]	C	T	4.590e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
2R	19400350	2R_19400350_SNP [dm3] 2R_23512827_SNP [dm6]	G	A	4.735e^-5	1	UPSTREAM CG3906 INTERGENIC
3L	14989083	3L_14989083_SNP [dm3] 3L_14995983_SNP [dm6]	C	G	4.784e^-5	1	INTRON Zip71B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	7766298	2R_7766298_SNP [dm3] 2R_11878793_SNP [dm6]	T	G	4.978e^-5	1	NON_SYNONYMOUS_CODING CG13185
3R	18002741	3R_18002741_SNP [dm3] 3R_22177019_SNP [dm6]	G	A	5.001e^-5	1	INTRON SKIP
2L	10061512	2L_10061512_SNP [dm3] 2L_10061512_SNP [dm6]	C	T	5.044e^-5	1	INTRON Spn31A
3L	2482496	3L_2482496_DEL [dm3] 3L_2482496_DEL [dm6]	AA	A	5.078e^-5	1	UPSTREAM CG45186 INTRON CG45186	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	21833505	3R_21833505_SNP [dm3] 3R_26007783_SNP [dm6]	T	C	5.094e^-5	1	UPSTREAM CR45039 INTERGENIC
3L	18934159	3L_18934159_SNP [dm3] 3L_18941059_SNP [dm6]	T	C	5.159e^-5	1	INTRON CG32204
2R	7766270	2R_7766270_SNP [dm3] 2R_11878765_SNP [dm6]	T	C	5.225e^-5	1	NON_SYNONYMOUS_CODING CG13185
2L	10315909	2L_10315909_SNP [dm3] 2L_10315909_SNP [dm6]	C	T	5.294e^-5	1	SYNONYMOUS_CODING CG4972	TF binding site mE1_TFBS_sens
2R	16525471	2R_16525471_SNP [dm3] 2R_20637966_SNP [dm6]	G	A	5.315e^-5	1	SYNONYMOUS_CODING CG13436 INTRON rig	TF binding site mE1_TFBS_sens
X	15059257	X_15059257_SNP [dm3] X_15165224_SNP [dm6]	G	A	5.494e^-5	1	INTERGENIC
2R	3292945	2R_3292945_SNP [dm3] 2R_7405440_SNP [dm6]	G	A	5.844e^-5	1	DOWNSTREAM CG43267 INTRON Eaf
2R	6383785	2R_6383785_SNP [dm3] 2R_10496280_SNP [dm6]	T	C	5.859e^-5	1	DOWNSTREAM lola INTRON lola
X	12318467	X_12318467_DEL [dm3] X_12424434_DEL [dm6]	AA	A	5.888e^-5	1	INTERGENIC
3L	8950547	3L_8950547_SNP [dm3] 3L_8957447_SNP [dm6]	A	G	5.990e^-5	1	SYNONYMOUS_CODING mRpL12 DOWNSTREAM GNBP3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	2262325	2L_2262325_SNP [dm3] 2L_2262325_SNP [dm6]	A	G	6.016e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	15816344	2R_15816344_SNP [dm3] 2R_19928839_SNP [dm6]	G	A	6.090e^-5	1	INTERGENIC
2L	9052209	2L_9052209_SNP [dm3] 2L_9052209_SNP [dm6]	T	C	6.196e^-5	1	UTR_3_PRIME CG31708
3R	11019578	3R_11019578_SNP [dm3] 3R_15193856_SNP [dm6]	G	C	6.346e^-5	1	SYNONYMOUS_CODING CG6752
2L	9052218	2L_9052218_SNP [dm3] 2L_9052218_SNP [dm6]	A	G	6.506e^-5	1	UTR_3_PRIME CG31708
3L	9399370	3L_9399370_SNP [dm3] 3L_9406270_SNP [dm6]	G	A	6.511e^-5	1	UTR_3_PRIME CG4022 DOWNSTREAM Cpr67B
2L	4185406	2L_4185406_INS [dm3] 2L_4185406_INS [dm6]	T	TCT	6.520e^-5	1	DOWNSTREAM CG31961 EXON CR44057
3L	6898825	3L_6898825_SNP [dm3] 3L_6905725_SNP [dm6]	C	G	6.612e^-5	1	INTERGENIC
3R	14057480	3R_14057480_SNP [dm3] 3R_18231758_SNP [dm6]	A	G	6.618e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	19567978	X_19567978_SNP [dm3] X_19673945_SNP [dm6]	A	T	6.623e^-5	1	INTRON et	transposable element FlyBase
2L	5338529	2L_5338529_SNP [dm3] 2L_5338529_SNP [dm6]	T	A	6.658e^-5	1	UPSTREAM fusl DOWNSTREAM CG12512 INTERGENIC
2R	3293005	2R_3293005_SNP [dm3] 2R_7405500_SNP [dm6]	C	T	6.711e^-5	1	INTRON Eaf
4	295734	4_295734_SNP [dm3] 4_275108_SNP [dm6]	G	C	6.757e^-5	1	INTRON NfI
3L	14082707	3L_14082707_SNP [dm3] 3L_14089607_SNP [dm6]	A	G	6.765e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	8373316	3R_8373316_SNP [dm3] 3R_12547594_SNP [dm6]	G	C	6.857e^-5	1	UTR_5_PRIME Octbeta3R
2R	20382329	2R_20382329_SNP [dm3] 2R_24494806_SNP [dm6]	T	C	6.911e^-5	1	SYNONYMOUS_CODING Crtp UPSTREAM CG13590	TF binding site mE1_TFBS_chinmo
3L	15790928	3L_15790928_SNP [dm3] 3L_15797828_SNP [dm6]	T	G	6.970e^-5	1	INTERGENIC
3R	12119546	3R_12119546_SNP [dm3] 3R_16293824_SNP [dm6]	T	A	6.998e^-5	1	INTRON gish
3L	5320661	3L_5320661_SNP [dm3] 3L_5327561_SNP [dm6]	G	A	7.023e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	7527214	2L_7527214_SNP [dm3] 2L_7527214_SNP [dm6]	G	A	7.323e^-5	1	INTRON RapGAP1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	4525177	X_4525177_SNP [dm3] X_4631144_SNP [dm6]	C	A	7.337e^-5	1	UTR_3_PRIME CG12179 UPSTREAM CG12184 DOWNSTREAM CG12179	transposable element FlyBase
2R	9627974	2R_9627974_SNP [dm3] 2R_13740469_SNP [dm6]	A	G	7.526e^-5	1	INTRON fas
2R	11173631	2R_11173631_SNP [dm3] 2R_15286126_SNP [dm6]	T	C	7.579e^-5	1	INTRON Trpm	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA

Showing 1 to 100 of 1,000 entries

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By genomic position
Variant impact
Gene name

md_Lifespan phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results