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=1.662e^-8)
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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2188 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
X	10185840	X_10185840_SNP [dm3] X_10291807_SNP [dm6]	G	T	2.537e^-6	0.822	INTRON alpha-Man-I
X	19158603	X_19158603_DEL [dm3] X_19264570_DEL [dm6]	TCCTATCTCTGTCT...	T	3.120e^-6	0.822	INTRON Vav	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	20919891	3R_20919891_SNP [dm3] 3R_25094169_SNP [dm6]	C	A	3.654e^-6	0.822	UPSTREAM fd96Cb INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	1773058	3L_1773058_SNP [dm3] 3L_1773058_SNP [dm6]	C	T	4.762e^-6	0.822	SYNONYMOUS_CODING CG13933 UPSTREAM CR44351	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	17348703	2R_17348703_SNP [dm3] 2R_21461198_SNP [dm6]	T	G	4.966e^-6	0.822	INTRON Sdc	TF binding site BDTNP1_TFBS_twi
3R	19565253	3R_19565253_SNP [dm3] 3R_23739531_SNP [dm6]	C	T	5.234e^-6	0.822	INTRON Hmgcr
3R	14550388	3R_14550388_SNP [dm3] 3R_18724666_SNP [dm6]	T	A	5.425e^-6	0.822	DOWNSTREAM CG7714 INTRON Cha
2R	8488811	2R_8488811_SNP [dm3] 2R_12601306_SNP [dm6]	G	A	6.653e^-6	0.822	INTRON Amph
2L	11843485	2L_11843485_SNP [dm3] 2L_11843485_SNP [dm6]	C	A	7.015e^-6	0.822	START_GAINED CG42486 UTR_5_PRIME CG42486 UTR_3_PRIME CG14933 UPSTREAM CG42486 INTRON Pde1c
3R	20919897	3R_20919897_SNP [dm3] 3R_25094175_SNP [dm6]	T	G	8.089e^-6	0.822	UPSTREAM fd96Cb INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	6245013	2L_6245013_SNP [dm3] 2L_6245013_SNP [dm6]	C	A	8.323e^-6	0.822	INTERGENIC
X	19158571	X_19158571_SNP [dm3] X_19264538_SNP [dm6]	T	A	9.348e^-6	0.822	INTRON Vav	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	26009899	3R_26009899_SNP [dm3] 3R_30184177_SNP [dm6]	C	T	1.010e^-5	0.822	EXON CR44262
2L	930406	2L_930406_SNP [dm3] 2L_930406_SNP [dm6]	T	C	1.148e^-5	0.822	SYNONYMOUS_CODING CG4341 INTRON CG4341
2L	11843480	2L_11843480_SNP [dm3] 2L_11843480_SNP [dm6]	C	A	1.196e^-5	0.822	UTR_5_PRIME CG42486 UTR_3_PRIME CG14933 UPSTREAM CG42486 INTRON Pde1c
2R	16731526	2R_16731526_SNP [dm3] 2R_20844021_SNP [dm6]	T	A	1.481e^-5	0.822	INTERGENIC
X	10185991	X_10185991_SNP [dm3] X_10291958_SNP [dm6]	T	G	1.585e^-5	0.822	INTRON alpha-Man-I
3L	7852125	3L_7852125_SNP [dm3] 3L_7859025_SNP [dm6]	T	C	1.587e^-5	0.822	INTRON Pdp1
2L	4514683	2L_4514683_SNP [dm3] 2L_4514683_SNP [dm6]	G	T	1.594e^-5	0.822	INTRON dp
3R	8598181	3R_8598181_SNP [dm3] 3R_12772459_SNP [dm6]	A	T	1.639e^-5	0.822	INTRON beat-Vc
3L	477095	3L_477095_SNP [dm3] 3L_477095_SNP [dm6]	A	T	1.677e^-5	0.822	INTRON klar
2R	4494841	2R_4494841_SNP [dm3] 2R_8607336_SNP [dm6]	A	T	1.785e^-5	0.822	INTRON rgr	TF binding site BDTNP1_TFBS_twi
2R	9123351	2R_9123351_SNP [dm3] 2R_13235846_SNP [dm6]	T	G	1.916e^-5	0.822	UPSTREAM CG4676 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	440468	2R_440468_INS [dm3] 2R_4552963_INS [dm6]	G	GG	1.920e^-5	0.822	INTRON Stlk	transposable element FlyBase
X	10186020	X_10186020_SNP [dm3] X_10291987_SNP [dm6]	A	T	1.926e^-5	0.822	INTRON alpha-Man-I
3L	4526321	3L_4526321_SNP [dm3] 3L_4526321_SNP [dm6]	T	G	1.974e^-5	0.822	INTRON Tie
X	7500735	X_7500735_SNP [dm3] X_7606702_SNP [dm6]	C	A	2.026e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	14678909	3R_14678909_DEL [dm3] 3R_18853187_DEL [dm6]	CC	C	2.027e^-5	0.822	INTERGENIC
X	5680455	X_5680455_SNP [dm3] X_5786422_SNP [dm6]	C	T	2.046e^-5	0.822	INTRON CG42699
X	10185982	X_10185982_SNP [dm3] X_10291949_SNP [dm6]	T	C	2.071e^-5	0.822	INTRON alpha-Man-I
3L	2419928	3L_2419928_SNP [dm3] 3L_2419928_SNP [dm6]	C	G	2.078e^-5	0.822	INTRON CG45186
2L	5403099	2L_5403099_SNP [dm3] 2L_5403099_SNP [dm6]	A	T	2.104e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
2L	5403108	2L_5403108_SNP [dm3] 2L_5403108_SNP [dm6]	C	A	2.104e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
2L	18463818	2L_18463818_SNP [dm3] 2L_18463818_SNP [dm6]	T	G	2.159e^-5	0.822	INTRON let-7-C
2L	128046	2L_128046_SNP [dm3] 2L_128046_SNP [dm6]	G	A	2.226e^-5	0.822	INTRON CG11455 & 1 other	TF binding site mE1_TFBS_Trl
3R	21368782	3R_21368782_SNP [dm3] 3R_25543060_SNP [dm6]	C	T	2.236e^-5	0.822	INTRON msi
3L	7852205	3L_7852205_SNP [dm3] 3L_7859105_SNP [dm6]	T	A	2.249e^-5	0.822	INTRON Pdp1
3L	16731038	3L_16731038_SNP [dm3] 3L_16737938_SNP [dm6]	T	C	2.295e^-5	0.822	SYNONYMOUS_CODING CG9701	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	17348707	2R_17348707_SNP [dm3] 2R_21461202_SNP [dm6]	C	T	2.296e^-5	0.822	INTRON Sdc	TF binding site BDTNP1_TFBS_twi
2R	17866509	2R_17866509_SNP [dm3] 2R_21979004_SNP [dm6]	C	T	2.375e^-5	0.822	SYNONYMOUS_CODING Gr58b UPSTREAM Gr58a	TF binding site mE1_TFBS_cad
3L	477181	3L_477181_SNP [dm3] 3L_477181_SNP [dm6]	T	C	2.392e^-5	0.822	INTRON klar
X	10186005	X_10186005_SNP [dm3] X_10291972_SNP [dm6]	C	G	2.475e^-5	0.822	INTRON alpha-Man-I
2R	17866493	2R_17866493_SNP [dm3] 2R_21978988_SNP [dm6]	G	A	2.492e^-5	0.822	SYNONYMOUS_CODING Gr58b UPSTREAM Gr58a	TF binding site mE1_TFBS_cad
3R	20919249	3R_20919249_SNP [dm3] 3R_25093527_SNP [dm6]	G	A	2.616e^-5	0.822	INTERGENIC
3L	681805	3L_681805_SNP [dm3] 3L_681805_SNP [dm6]	G	A	2.620e^-5	0.822	INTRON CG3386	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	4818388	2L_4818388_SNP [dm3] 2L_4818388_SNP [dm6]	C	A	2.797e^-5	0.822	UPSTREAM mir-4910 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	7500744	X_7500744_SNP [dm3] X_7606711_SNP [dm6]	T	G	2.850e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	26058153	3R_26058153_SNP [dm3] 3R_30232431_SNP [dm6]	C	A	2.855e^-5	0.822	INTERGENIC
3L	6542226	3L_6542226_SNP [dm3] 3L_6549126_SNP [dm6]	A	T	2.896e^-5	0.822	UTR_3_PRIME sfl
2R	4493405	2R_4493405_SNP [dm3] 2R_8605900_SNP [dm6]	A	T	2.900e^-5	0.822	INTRON rgr	TF binding site mE1_TFBS_cad
3L	483650	3L_483650_SNP [dm3] 3L_483650_SNP [dm6]	G	T	3.050e^-5	0.822	INTRON klar
2L	4546212	2L_4546212_SNP [dm3] 2L_4546212_SNP [dm6]	G	C	3.054e^-5	0.822	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	19041122	3R_19041122_SNP [dm3] 3R_23215400_SNP [dm6]	G	A	3.068e^-5	0.822	UPSTREAM cnc INTRON cnc	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	18943066	2R_18943066_SNP [dm3] 2R_23055543_SNP [dm6]	T	C	3.084e^-5	0.822	UTR_5_PRIME CG44252	TF binding site BDTNP1_TFBS_twi
3L	6068385	3L_6068385_SNP [dm3] 3L_6075285_SNP [dm6]	G	C	3.088e^-5	0.822	UPSTREAM CG6610 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens
2L	10422256	2L_10422256_SNP [dm3] 2L_10422256_SNP [dm6]	G	A	3.104e^-5	0.822	SYNONYMOUS_CODING pie	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	19041115	3R_19041115_SNP [dm3] 3R_23215393_SNP [dm6]	G	T	3.133e^-5	0.822	UPSTREAM cnc INTRON cnc	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	4503437	2L_4503437_SNP [dm3] 2L_4503437_SNP [dm6]	G	A	3.143e^-5	0.822	NON_SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	7852135	3L_7852135_SNP [dm3] 3L_7859035_SNP [dm6]	G	C	3.217e^-5	0.822	INTRON Pdp1
2L	4534022	2L_4534022_SNP [dm3] 2L_4534022_SNP [dm6]	C	A	3.368e^-5	0.822	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_sens
3L	494797	3L_494797_INS [dm3] 3L_494797_INS [dm6]	A	AA	3.394e^-5	0.822	INTRON klar
3R	13781149	3R_13781149_SNP [dm3] 3R_17955427_SNP [dm6]	A	C	3.405e^-5	0.822	INTRON cpo
3R	26923909	3R_26923909_SNP [dm3] 3R_31098187_SNP [dm6]	G	A	3.425e^-5	0.822	UPSTREAM CG11317 DOWNSTREAM CG15553 INTERGENIC
X	14379696	X_14379696_SNP [dm3] X_14485663_SNP [dm6]	C	T	3.466e^-5	0.822	INTERGENIC
X	7500733	X_7500733_SNP [dm3] X_7606700_SNP [dm6]	G	T	3.499e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	18269237	2L_18269237_SNP [dm3] 2L_18269237_SNP [dm6]	C	T	3.535e^-5	0.822	INTRON CG42750
2L	4507910	2L_4507910_SNP [dm3] 2L_4507910_SNP [dm6]	A	G	3.648e^-5	0.822	INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	14742959	X_14742959_SNP [dm3] X_14848926_SNP [dm6]	G	C	3.699e^-5	0.822	UPSTREAM CG9522 INTRON Flo2
X	8274947	X_8274947_SNP [dm3] X_8380914_SNP [dm6]	T	C	3.753e^-5	0.822	INTERGENIC
X	9462017	X_9462017_SNP [dm3] X_9567984_SNP [dm6]	A	T	3.849e^-5	0.822	SYNONYMOUS_CODING Cubn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	9280176	2L_9280176_SNP [dm3] 2L_9280176_SNP [dm6]	T	G	4.003e^-5	0.822	INTRON Ggamma30A
2R	6638139	2R_6638139_SNP [dm3] 2R_10750634_SNP [dm6]	C	T	4.032e^-5	0.822	INTRON CG33144
X	20878385	X_20878385_SNP [dm3] X_21007358_SNP [dm6]	A	C	4.039e^-5	0.822	INTERGENIC
2L	9279998	2L_9279998_SNP [dm3] 2L_9279998_SNP [dm6]	G	T	4.054e^-5	0.822	INTRON Ggamma30A
3L	2582606	3L_2582606_SNP [dm3] 3L_2582606_SNP [dm6]	A	G	4.111e^-5	0.822	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10622994	2L_10622994_SNP [dm3] 2L_10622994_SNP [dm6]	T	C	4.181e^-5	0.822	INTRON Trim9
2R	7286655	2R_7286655_SNP [dm3] 2R_11399150_SNP [dm6]	T	C	4.229e^-5	0.822	DOWNSTREAM tRNA:CR30506 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	459174	2R_459174_INS [dm3] 2R_4571669_INS [dm6]	A	ATTAAA	4.374e^-5	0.822	INTERGENIC	TF binding site mE1_TFBS_inv
3L	5238270	3L_5238270_SNP [dm3] 3L_5245170_SNP [dm6]	A	G	4.427e^-5	0.822	INTRON shep
2L	5403133	2L_5403133_SNP [dm3] 2L_5403133_SNP [dm6]	A	G	4.554e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA
2L	17898302	2L_17898302_SNP [dm3] 2L_17898302_SNP [dm6]	G	C	4.591e^-5	0.822	INTERGENIC
X	7500737	X_7500737_SNP [dm3] X_7606704_SNP [dm6]	T	C	4.678e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2R	14990262	2R_14990262_SNP [dm3] 2R_19102757_SNP [dm6]	G	C	4.735e^-5	0.822	INTRON 5-HT1A
X	10185979	X_10185979_SNP [dm3] X_10291946_SNP [dm6]	T	G	4.762e^-5	0.822	INTRON alpha-Man-I
2L	17593895	2L_17593895_SNP [dm3] 2L_17593895_SNP [dm6]	A	T	4.774e^-5	0.822	UPSTREAM Sytalpha INTRON Sytalpha
X	9557557	X_9557557_SNP [dm3] X_9663524_SNP [dm6]	A	G	4.795e^-5	0.822	UPSTREAM CG3106 INTERGENIC
2L	11184073	2L_11184073_SNP [dm3] 2L_11184073_SNP [dm6]	T	G	4.811e^-5	0.822	INTRON Ca-beta
X	7500767	X_7500767_SNP [dm3] X_7606734_SNP [dm6]	A	G	4.838e^-5	0.822	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
3R	21122066	3R_21122066_SNP [dm3] 3R_25296344_SNP [dm6]	G	A	4.849e^-5	0.822	SYNONYMOUS_CODING CG31097 UPSTREAM CG31102
3R	9226136	3R_9226136_DEL [dm3] 3R_13400414_DEL [dm6]	TTAGTTAT	T	4.914e^-5	0.822	INTRON CG9796
X	14997932	X_14997932_SNP [dm3] X_15103899_SNP [dm6]	A	G	4.923e^-5	0.822	INTRON Rab3-GEF
2R	8133130	2R_8133130_SNP [dm3] 2R_12245625_SNP [dm6]	G	C	4.944e^-5	0.822	UPSTREAM CG43244 INTERGENIC
3L	3021380	3L_3021380_SNP [dm3] 3L_3021380_SNP [dm6]	C	T	4.986e^-5	0.822	INTERGENIC
2L	7330328	2L_7330328_SNP [dm3] 2L_7330328_SNP [dm6]	A	T	5.002e^-5	0.822	UPSTREAM CR45304 INTERGENIC
X	3959211	X_3959211_SNP [dm3] X_4065178_SNP [dm6]	G	C	5.052e^-5	0.822	INTERGENIC
2L	6153156	2L_6153156_SNP [dm3] 2L_6153156_SNP [dm6]	G	A	5.143e^-5	0.822	NON_SYNONYMOUS_CODING Muc26B DOWNSTREAM CG31639	TF binding site BDTNP1_TFBS_sna
3L	16450014	3L_16450014_SNP [dm3] 3L_16456914_SNP [dm6]	T	G	5.149e^-5	0.822	INTRON CG33158
3L	9808729	3L_9808729_SNP [dm3] 3L_9815629_SNP [dm6]	A	G	5.169e^-5	0.822	UPSTREAM CG43897 INTRON CG43897
3L	2538190	3L_2538190_DEL [dm3] 3L_2538190_DEL [dm6]	AGA	A	5.225e^-5	0.822	INTRON Spn
3R	14544537	3R_14544537_SNP [dm3] 3R_18718815_SNP [dm6]	C	T	5.231e^-5	0.822	UTR_3_PRIME VAChT INTRON Cha

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Nuclear_Depth_Cov phenotype

Phenotype distribution and association to known covariates

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GWAS results