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=2.845e^-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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	4.7879	0.0287

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1620 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
3R	4331250	3R_4331250_SNP [dm3] 3R_8505528_SNP [dm6]	T	G	8.687e^-7	0.984	INTERGENIC	TF binding site mE1_TFBS_cad
3L	17853812	3L_17853812_SNP [dm3] 3L_17860712_SNP [dm6]	C	G	5.036e^-6	0.984	DOWNSTREAM CG34002 INTERGENIC
X	1354610	X_1354610_INS [dm3] X_1460577_INS [dm6]	T	TA	5.061e^-6	0.984	UTR_5_PRIME CG14786 DOWNSTREAM CG14787	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_run
2R	11688234	2R_11688234_SNP [dm3] 2R_15800729_SNP [dm6]	C	A	5.438e^-6	0.984	INTRON Zasp52 & 1 other
2R	16295473	2R_16295473_SNP [dm3] 2R_20407968_SNP [dm6]	C	T	6.961e^-6	0.984	INTERGENIC
3L	15285419	3L_15285419_SNP [dm3] 3L_15292319_SNP [dm6]	C	G	7.706e^-6	0.984	INTERGENIC
3L	16962274	3L_16962274_SNP [dm3] 3L_16969174_SNP [dm6]	T	A	7.720e^-6	0.984	UPSTREAM Exn DOWNSTREAM Nc73EF INTERGENIC
3L	16962282	3L_16962282_SNP [dm3] 3L_16969182_SNP [dm6]	T	G	7.720e^-6	0.984	UPSTREAM Exn DOWNSTREAM Nc73EF INTERGENIC
2R	14366869	2R_14366869_SNP [dm3] 2R_18479364_SNP [dm6]	T	A	7.863e^-6	0.984	INTRON CG30116
3L	17853328	3L_17853328_SNP [dm3] 3L_17860228_SNP [dm6]	T	G	9.658e^-6	0.984	SYNONYMOUS_CODING CG34002
3L	3493158	3L_3493158_SNP [dm3] 3L_3493158_SNP [dm6]	T	C	9.835e^-6	0.984	INTRON CG42324
2R	9740764	2R_9740764_SNP [dm3] 2R_13853259_SNP [dm6]	C	G	1.118e^-5	0.984	SYNONYMOUS_CODING CG6543 DOWNSTREAM CG30485	TF binding site BDTNP1_TFBS_gt BDTNP1_TFBS_sna mE1_TFBS_inv
3L	17850683	3L_17850683_SNP [dm3] 3L_17857583_SNP [dm6]	C	T	1.129e^-5	0.984	UPSTREAM CG5535 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Trl
X	5828615	X_5828615_SNP [dm3] X_5934582_SNP [dm6]	T	C	1.196e^-5	0.984	INTRON CG3726
2R	14749940	2R_14749940_SNP [dm3] 2R_18862435_SNP [dm6]	A	T	1.372e^-5	0.984	UPSTREAM CG43069 & 1 other INTERGENIC
2R	19644659	2R_19644659_SNP [dm3] 2R_23757136_SNP [dm6]	C	A	1.405e^-5	0.984	NON_SYNONYMOUS_CODING CG9850 INTRON CG9850
2R	19323714	2R_19323714_SNP [dm3] 2R_23436191_SNP [dm6]	T	A	1.414e^-5	0.984	INTERGENIC
2R	14749941	2R_14749941_SNP [dm3] 2R_18862436_SNP [dm6]	A	T	1.471e^-5	0.984	UPSTREAM CG43069 & 1 other INTERGENIC
2R	14366894	2R_14366894_DEL [dm3] 2R_18479389_DEL [dm6]	AA	T	1.497e^-5	0.984	INTRON CG30116
3L	18789180	3L_18789180_SNP [dm3] 3L_18796080_SNP [dm6]	G	C	1.596e^-5	0.984	INTRON ftz-f1
3L	7628925	3L_7628925_SNP [dm3] 3L_7635825_SNP [dm6]	G	A	1.610e^-5	0.984	INTRON CG33275	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	6903921	3R_6903921_SNP [dm3] 3R_11078199_SNP [dm6]	T	C	1.670e^-5	0.984	INTERGENIC
2L	12486790	2L_12486790_SNP [dm3] 2L_12486790_SNP [dm6]	A	G	1.697e^-5	0.984	INTRON bun
3L	10115037	3L_10115037_SNP [dm3] 3L_10121937_SNP [dm6]	C	T	1.769e^-5	0.984	INTRON dpr6
2R	14414383	2R_14414383_SNP [dm3] 2R_18526878_SNP [dm6]	C	T	1.824e^-5	0.984	UPSTREAM CG10924 DOWNSTREAM CG43066 INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	8563519	2R_8563519_SNP [dm3] 2R_12676014_SNP [dm6]	T	G	1.937e^-5	0.984	UPSTREAM CG42708 INTRON CG42708	TF binding site mE1_TFBS_inv
2L	9630107	2L_9630107_SNP [dm3] 2L_9630107_SNP [dm6]	T	C	1.973e^-5	0.984	INTERGENIC
2R	12170376	2R_12170376_SNP [dm3] 2R_16282871_SNP [dm6]	G	A	2.499e^-5	0.984	UTR_5_PRIME CG7755 UPSTREAM CG9068	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	4201351	3R_4201351_SNP [dm3] 3R_8375629_SNP [dm6]	A	G	2.896e^-5	0.984	INTRON CG45263
2R	14749944	2R_14749944_SNP [dm3] 2R_18862439_SNP [dm6]	G	T	2.902e^-5	0.984	UPSTREAM CG43069 & 1 other INTERGENIC
3R	25787209	3R_25787209_SNP [dm3] 3R_29961487_SNP [dm6]	C	T	2.953e^-5	0.984	INTRON TkR99D
3L	22367622	3L_22367622_SNP [dm3] 3L_22374522_SNP [dm6]	C	A	3.003e^-5	0.984	INTRON Ten-m	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	4659122	3L_4659122_INS [dm3] 3L_4659122_INS [dm6]	A	TTG	3.121e^-5	0.984	INTRON axo
3L	8673546	3L_8673546_SNP [dm3] 3L_8680446_SNP [dm6]	G	A	3.304e^-5	0.984	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
3R	12433763	3R_12433763_SNP [dm3] 3R_16608041_SNP [dm6]	T	C	3.365e^-5	0.984	INTERGENIC
3R	6590222	3R_6590222_SNP [dm3] 3R_10764500_SNP [dm6]	C	T	3.386e^-5	0.984	SYNONYMOUS_CODING Cap-H2
X	5468501	X_5468501_SNP [dm3] X_5574468_SNP [dm6]	C	T	3.652e^-5	0.984	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	11664253	3L_11664253_SNP [dm3] 3L_11671153_SNP [dm6]	T	C	3.664e^-5	0.984	INTRON CG32085
3R	10801736	3R_10801736_SNP [dm3] 3R_14976014_SNP [dm6]	C	T	3.670e^-5	0.984	INTERGENIC
3L	2437872	3L_2437872_SNP [dm3] 3L_2437872_SNP [dm6]	C	T	3.714e^-5	0.984	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_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
3L	11221708	3L_11221708_SNP [dm3] 3L_11228608_SNP [dm6]	T	C	3.739e^-5	0.984	DOWNSTREAM CG42671 INTRON CG42671
3R	14631431	3R_14631431_SNP [dm3] 3R_18805709_SNP [dm6]	G	C	3.989e^-5	0.984	UTR_3_PRIME CG18208
2L	2969058	2L_2969058_SNP [dm3] 2L_2969058_SNP [dm6]	G	A	4.086e^-5	0.984	SYNONYMOUS_CODING Ts DOWNSTREAM Rbp9 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	5828644	X_5828644_SNP [dm3] X_5934611_SNP [dm6]	G	A	4.096e^-5	0.984	INTRON CG3726
3L	17867107	3L_17867107_SNP [dm3] 3L_17874007_SNP [dm6]	T	C	4.136e^-5	0.984	UPSTREAM CR43087 INTERGENIC	TF binding site mE1_TFBS_Trl transposable element FlyBase
2R	16654310	2R_16654310_SNP [dm3] 2R_20766805_SNP [dm6]	G	T	4.340e^-5	0.984	DOWNSTREAM CR44665 EXON CR44665
3L	15285245	3L_15285245_SNP [dm3] 3L_15292145_SNP [dm6]	C	T	4.356e^-5	0.984	INTERGENIC
3R	6590256	3R_6590256_SNP [dm3] 3R_10764534_SNP [dm6]	G	A	4.385e^-5	0.984	NON_SYNONYMOUS_CODING Cap-H2
3L	14215711	3L_14215711_SNP [dm3] 3L_14222611_SNP [dm6]	A	T	4.452e^-5	0.984	INTRON nuf
2R	19622832	2R_19622832_SNP [dm3] 2R_23735309_SNP [dm6]	C	A	4.470e^-5	0.984	UTR_3_PRIME egl DOWNSTREAM Sesn
3L	5430349	3L_5430349_INS [dm3] 3L_5437249_INS [dm6]	T	TT	4.831e^-5	0.984	INTRON CG34391
2R	15188894	2R_15188894_SNP [dm3] 2R_19301389_SNP [dm6]	C	T	4.841e^-5	0.984	INTRON Tab2	TF binding site mE1_TFBS_inv
2R	15188897	2R_15188897_SNP [dm3] 2R_19301392_SNP [dm6]	A	G	4.841e^-5	0.984	INTRON Tab2	TF binding site mE1_TFBS_inv
2L	7651197	2L_7651197_SNP [dm3] 2L_7651197_SNP [dm6]	A	C	5.033e^-5	0.984	INTRON Slob
2L	10629949	2L_10629949_SNP [dm3] 2L_10629949_SNP [dm6]	T	C	5.234e^-5	0.984	SYNONYMOUS_CODING CG7329
2L	2186921	2L_2186921_SNP [dm3] 2L_2186921_SNP [dm6]	T	C	5.363e^-5	0.984	UPSTREAM tRNA:CR31946 DOWNSTREAM CR44066 INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	11304795	2R_11304795_SNP [dm3] 2R_15417290_SNP [dm6]	T	A	5.447e^-5	0.984	INTRON CG43729
3L	9944688	3L_9944688_SNP [dm3] 3L_9951588_SNP [dm6]	T	C	5.500e^-5	0.984	INTRON CG34356
3L	17866379	3L_17866379_SNP [dm3] 3L_17873279_SNP [dm6]	T	G	5.655e^-5	0.984	INTERGENIC	transposable element FlyBase
3L	6496851	3L_6496851_SNP [dm3] 3L_6503751_SNP [dm6]	C	T	5.679e^-5	0.984	INTRON sfl	TF binding site BDTNP1_TFBS_dl
3L	21261293	3L_21261293_SNP [dm3] 3L_21268193_SNP [dm6]	C	A	5.765e^-5	0.984	UPSTREAM CR45162 & 1 other DOWNSTREAM CG9389 INTRON CG9391
3L	11590825	3L_11590825_SNP [dm3] 3L_11597725_SNP [dm6]	A	T	5.777e^-5	0.984	INTRON CG7368
2R	11304797	2R_11304797_SNP [dm3] 2R_15417292_SNP [dm6]	C	T	5.844e^-5	0.984	INTRON CG43729
2L	2786334	2L_2786334_DEL [dm3] 2L_2786334_DEL [dm6]	AA	A	5.966e^-5	0.984	INTRON Syt1
2L	2882567	2L_2882567_SNP [dm3] 2L_2882567_SNP [dm6]	G	A	6.023e^-5	0.984	SYNONYMOUS_CODING NTPase INTRON NTPase	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	3703864	3R_3703864_SNP [dm3] 3R_7878142_SNP [dm6]	A	G	6.030e^-5	0.984	INTRON CG17816
2L	10630463	2L_10630463_SNP [dm3] 2L_10630463_SNP [dm6]	T	C	6.075e^-5	0.984	SYNONYMOUS_CODING CG7329	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	21823957	3L_21823957_SNP [dm3] 3L_21830857_SNP [dm6]	A	C	6.179e^-5	0.984	NON_SYNONYMOUS_CODING CG7148 UPSTREAM CR43309	TF binding site mE1_TFBS_cad
3L	21835297	3L_21835297_DEL [dm3] 3L_21842197_DEL [dm6]	GCTG	G	6.179e^-5	0.984	CODON_DELETION CG14563 UPSTREAM P5CDh1	TF binding site BDTNP1_TFBS_dl
3L	21840219	3L_21840219_SNP [dm3] 3L_21847119_SNP [dm6]	T	G	6.179e^-5	0.984	INTRON mub
3L	21845479	3L_21845479_SNP [dm3] 3L_21852379_SNP [dm6]	C	T	6.179e^-5	0.984	INTRON mub
3R	6591817	3R_6591817_SNP [dm3] 3R_10766095_SNP [dm6]	T	G	6.316e^-5	0.984	SYNONYMOUS_CODING Cap-H2 UTR_3_PRIME Cap-H2 DOWNSTREAM TfIIFbeta
3R	6591819	3R_6591819_SNP [dm3] 3R_10766097_SNP [dm6]	G	A	6.316e^-5	0.984	NON_SYNONYMOUS_CODING Cap-H2 UTR_3_PRIME Cap-H2 DOWNSTREAM TfIIFbeta
3L	11590702	3L_11590702_DEL [dm3] 3L_11597602_DEL [dm6]	GT	C	6.338e^-5	0.984	INTRON CG7368
3L	8443510	3L_8443510_SNP [dm3] 3L_8450410_SNP [dm6]	G	T	6.342e^-5	0.984	UTR_5_PRIME Gug UPSTREAM Gug	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
3L	1682411	3L_1682411_SNP [dm3] 3L_1682411_SNP [dm6]	C	T	6.443e^-5	0.984	INTRON CG7991
2L	7651223	2L_7651223_SNP [dm3] 2L_7651223_SNP [dm6]	C	T	6.505e^-5	0.984	INTRON Slob
2R	9337480	2R_9337480_SNP [dm3] 2R_13449975_SNP [dm6]	A	G	6.560e^-5	0.984	UPSTREAM cnn & 1 other INTRON cnn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl mE1_TFBS_Ubx
3L	14215710	3L_14215710_SNP [dm3] 3L_14222610_SNP [dm6]	G	T	6.580e^-5	0.984	INTRON nuf
2R	16224522	2R_16224522_SNP [dm3] 2R_20337017_SNP [dm6]	A	T	6.617e^-5	0.984	INTERGENIC
3R	22560061	3R_22560061_SNP [dm3] 3R_26734339_SNP [dm6]	G	A	6.639e^-5	0.984	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	15443178	2R_15443178_SNP [dm3] 2R_19555673_SNP [dm6]	T	C	6.684e^-5	0.984	INTRON sm	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	7004724	3L_7004724_SNP [dm3] 3L_7011624_SNP [dm6]	G	A	6.862e^-5	0.984	INTRON Mp
3L	17882423	3L_17882423_SNP [dm3] 3L_17889323_SNP [dm6]	C	T	7.043e^-5	0.984	SPLICE_SITE_REGION CG7402 INTRON CG7402
2R	11304715	2R_11304715_SNP [dm3] 2R_15417210_SNP [dm6]	A	C	7.163e^-5	0.984	INTRON CG43729
2R	11304730	2R_11304730_SNP [dm3] 2R_15417225_SNP [dm6]	T	A	7.163e^-5	0.984	INTRON CG43729
2R	11304731	2R_11304731_SNP [dm3] 2R_15417226_SNP [dm6]	A	T	7.163e^-5	0.984	INTRON CG43729
2R	11304743	2R_11304743_SNP [dm3] 2R_15417238_SNP [dm6]	A	C	7.163e^-5	0.984	INTRON CG43729
2R	11304747	2R_11304747_SNP [dm3] 2R_15417242_SNP [dm6]	T	A	7.163e^-5	0.984	INTRON CG43729
3L	4659254	3L_4659254_SNP [dm3] 3L_4659254_SNP [dm6]	A	T	7.303e^-5	0.984	INTRON axo
3R	14449333	3R_14449333_SNP [dm3] 3R_18623611_SNP [dm6]	C	A	7.480e^-5	0.984	INTRON qin
3R	17218855	3R_17218855_SNP [dm3] 3R_21393133_SNP [dm6]	T	A	7.524e^-5	0.984	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3L	9563296	3L_9563296_INS [dm3] 3L_9570196_INS [dm6]	C	CC	7.548e^-5	0.984	INTRON CG42673
3L	15285144	3L_15285144_SNP [dm3] 3L_15292044_SNP [dm6]	A	G	7.679e^-5	0.984	INTERGENIC
2L	19818313	2L_19818313_SNP [dm3] 2L_19818313_SNP [dm6]	A	T	7.707e^-5	0.984	INTRON sick	transposable element FlyBase
2R	9337481	2R_9337481_SNP [dm3] 2R_13449976_SNP [dm6]	T	C	7.713e^-5	0.984	UPSTREAM cnn & 1 other INTRON cnn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl mE1_TFBS_Ubx
3L	18838906	3L_18838906_SNP [dm3] 3L_18845806_SNP [dm6]	C	A	7.731e^-5	0.984	INTRON Indy	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	11590742	3L_11590742_SNP [dm3] 3L_11597642_SNP [dm6]	G	A	7.786e^-5	0.984	INTRON CG7368
3L	11590758	3L_11590758_SNP [dm3] 3L_11597658_SNP [dm6]	A	T	7.786e^-5	0.984	INTRON CG7368
3L	11590769	3L_11590769_DEL [dm3] 3L_11597669_DEL [dm6]	CA	C	7.786e^-5	0.984	INTRON CG7368

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

Missing results

By genomic position
Variant impact
Gene name

pc_KP_PElem_HC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results