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=2.078e^-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
In_3R_Mo	0.036517

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_Mo	3.7532	0.0527

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1064 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
2L	16665677	2L_16665677_SNP [dm3] 2L_16665677_SNP [dm6]	G	C	1.977e^-6	0.935	INTRON Trpgamma	transposable element FlyBase
X	6455644	X_6455644_SNP [dm3] X_6561611_SNP [dm6]	G	C	9.581e^-6	0.935	INTRON CG34417	TF binding site mE1_TFBS_sens
2L	16665679	2L_16665679_SNP [dm3] 2L_16665679_SNP [dm6]	G	T	1.042e^-5	0.935	INTRON Trpgamma	transposable element FlyBase
3R	1807153	3R_1807153_SNP [dm3] 3R_5981431_SNP [dm6]	G	A	1.186e^-5	0.935	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	10995524	2L_10995524_SNP [dm3] 2L_10995524_SNP [dm6]	G	T	1.259e^-5	0.935	UTR_3_PRIME CG16833 DOWNSTREAM CG16833 INTRON CG16833
3L	6372137	3L_6372137_SNP [dm3] 3L_6379037_SNP [dm6]	T	A	1.663e^-5	0.935	INTERGENIC
X	6455411	X_6455411_SNP [dm3] X_6561378_SNP [dm6]	A	G	1.850e^-5	0.935	SYNONYMOUS_CODING CG34417
X	6455531	X_6455531_SNP [dm3] X_6561498_SNP [dm6]	G	A	1.877e^-5	0.935	SYNONYMOUS_CODING CG34417	TF binding site mE1_TFBS_sens
3R	15241640	3R_15241640_SNP [dm3] 3R_19415918_SNP [dm6]	C	T	1.916e^-5	0.935	START_GAINED CG31221 UTR_5_PRIME CG31221
2L	9724105	2L_9724105_SNP [dm3] 2L_9724105_SNP [dm6]	G	T	2.078e^-5	0.935	INTRON Nckx30C
2R	19849634	2R_19849634_SNP [dm3] 2R_23962111_SNP [dm6]	T	C	2.390e^-5	0.935	UPSTREAM Fmo-1 DOWNSTREAM alpha-catenin-related INTRON CG13566
2R	5504251	2R_5504251_SNP [dm3] 2R_9616746_SNP [dm6]	T	C	2.704e^-5	0.935	INTRON Mmp2
3R	18984689	3R_18984689_SNP [dm3] 3R_23158967_SNP [dm6]	G	A	3.000e^-5	0.935	SYNONYMOUS_CODING VhaAC39-2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
3R	10600659	3R_10600659_SNP [dm3] 3R_14774937_SNP [dm6]	T	A	3.046e^-5	0.935	INTRON jvl
3R	10600664	3R_10600664_SNP [dm3] 3R_14774942_SNP [dm6]	C	A	3.046e^-5	0.935	INTRON jvl
X	13923955	X_13923955_SNP [dm3] X_14029922_SNP [dm6]	A	T	3.074e^-5	0.935	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	13923970	X_13923970_SNP [dm3] X_14029937_SNP [dm6]	C	G	3.074e^-5	0.935	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15967419	3R_15967419_SNP [dm3] 3R_20141697_SNP [dm6]	C	A	3.096e^-5	0.935	INTERGENIC
3L	11639744	3L_11639744_SNP [dm3] 3L_11646644_SNP [dm6]	C	T	3.275e^-5	0.935	SYNONYMOUS_CODING RIOK1 UPSTREAM CG6071
X	6455732	X_6455732_SNP [dm3] X_6561699_SNP [dm6]	A	G	3.829e^-5	0.935	SYNONYMOUS_CODING CG34417	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	10995579	2L_10995579_SNP [dm3] 2L_10995579_SNP [dm6]	T	C	3.934e^-5	0.935	UTR_3_PRIME CG16833 DOWNSTREAM CG16833 INTRON CG16833
2L	10995723	2L_10995723_SNP [dm3] 2L_10995723_SNP [dm6]	G	T	4.104e^-5	0.935	UTR_3_PRIME CG16833 DOWNSTREAM CG16833 INTRON CG16833
2L	9457217	2L_9457217_SNP [dm3] 2L_9457217_SNP [dm6]	A	C	4.344e^-5	0.935	INTRON numb	TF binding site mE1_TFBS_sens
2R	10286749	2R_10286749_SNP [dm3] 2R_14399244_SNP [dm6]	A	G	4.387e^-5	0.935	INTERGENIC
2L	10441512	2L_10441512_SNP [dm3] 2L_10441512_SNP [dm6]	C	T	4.621e^-5	0.935	DOWNSTREAM CG13142 & 1 other INTERGENIC
3L	18933721	3L_18933721_SNP [dm3] 3L_18940621_SNP [dm6]	C	G	4.785e^-5	0.935	INTRON CG32204
3L	10667158	3L_10667158_SNP [dm3] 3L_10674058_SNP [dm6]	G	C	4.965e^-5	0.935	INTRON simj	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	2924383	2L_2924383_INS [dm3] 2L_2924383_INS [dm6]	G	GGG	5.025e^-5	0.935	INTRON lilli
2L	10995745	2L_10995745_SNP [dm3] 2L_10995745_SNP [dm6]	T	C	5.114e^-5	0.935	UTR_3_PRIME CG16833 DOWNSTREAM CG16833 INTRON CG16833
2L	8323937	2L_8323937_SNP [dm3] 2L_8323937_SNP [dm6]	A	G	5.320e^-5	0.935	INTRON CG7781
2R	5791901	2R_5791901_SNP [dm3] 2R_9904396_SNP [dm6]	G	C	5.556e^-5	0.935	INTERGENIC	enhancer mE1_CBP_Enhancers
2R	10286809	2R_10286809_SNP [dm3] 2R_14399304_SNP [dm6]	A	G	5.732e^-5	0.935	INTERGENIC
2R	10286811	2R_10286811_SNP [dm3] 2R_14399306_SNP [dm6]	T	G	5.732e^-5	0.935	INTERGENIC
3L	22334722	3L_22334722_SNP [dm3] 3L_22341622_SNP [dm6]	G	A	6.216e^-5	0.935	INTRON Ten-m
3L	13886119	3L_13886119_SNP [dm3] 3L_13893019_SNP [dm6]	G	A	6.702e^-5	0.935	INTRON dysc
3L	13886123	3L_13886123_SNP [dm3] 3L_13893023_SNP [dm6]	A	C	6.702e^-5	0.935	INTRON dysc
X	4490379	X_4490379_SNP [dm3] X_4596346_SNP [dm6]	C	T	6.795e^-5	0.935	INTRON CR32773	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	16382760	2L_16382760_SNP [dm3] 2L_16382760_SNP [dm6]	C	T	6.861e^-5	0.935	INTERGENIC
2R	3228744	2R_3228744_DEL [dm3] 2R_7341239_DEL [dm6]	GG	G	7.094e^-5	0.935	SPLICE_SITE_REGION Dscam1 INTRON Dscam1
2L	16382898	2L_16382898_SNP [dm3] 2L_16382898_SNP [dm6]	A	C	7.507e^-5	0.935	INTERGENIC
2R	5726508	2R_5726508_SNP [dm3] 2R_9839003_SNP [dm6]	A	G	7.507e^-5	0.935	SYNONYMOUS_CODING Lsm11 UPSTREAM CG1665 DOWNSTREAM CG1663	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_sens
3L	15986238	3L_15986238_INS [dm3] 3L_15993138_INS [dm6]	A	AA	7.657e^-5	0.935	UTR_3_PRIME CG5830 DOWNSTREAM Hip14	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	16429744	2R_16429744_SNP [dm3] 2R_20542239_SNP [dm6]	G	A	7.923e^-5	0.935	UPSTREAM CR44652 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	6455420	X_6455420_SNP [dm3] X_6561387_SNP [dm6]	C	T	8.034e^-5	0.935	SYNONYMOUS_CODING CG34417
3L	12538647	3L_12538647_SNP [dm3] 3L_12545547_SNP [dm6]	C	A	8.045e^-5	0.935	INTRON sowah
3L	13886256	3L_13886256_SNP [dm3] 3L_13893156_SNP [dm6]	T	A	8.078e^-5	0.935	INTRON dysc
2L	6681415	2L_6681415_SNP [dm3] 2L_6681415_SNP [dm6]	T	G	8.257e^-5	0.935	INTRON Nhe3	TF binding site mE1_TFBS_inv
3R	19596781	3R_19596781_SNP [dm3] 3R_23771059_SNP [dm6]	A	G	9.054e^-5	0.935	SYNONYMOUS_CODING tst	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	10667029	3L_10667029_SNP [dm3] 3L_10673929_SNP [dm6]	T	G	9.361e^-5	0.935	INTRON simj	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	19597042	3R_19597042_SNP [dm3] 3R_23771320_SNP [dm6]	T	C	9.685e^-5	0.935	SYNONYMOUS_CODING tst
3L	16854941	3L_16854941_SNP [dm3] 3L_16861841_SNP [dm6]	A	G	9.723e^-5	0.935	DOWNSTREAM CG13029 INTRON Rh4	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_ttk
3L	18151802	3L_18151802_SNP [dm3] 3L_18158702_SNP [dm6]	A	C	9.738e^-5	0.935	INTRON CG13699	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	18572953	X_18572953_SNP [dm3] X_18678920_SNP [dm6]	C	G	9.770e^-5	0.935	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	17891927	3L_17891927_SNP [dm3] 3L_17898827_SNP [dm6]	T	C	1.005e^-4	0.935	DOWNSTREAM Prestin INTERGENIC
X	9227993	X_9227993_SNP [dm3] X_9333960_SNP [dm6]	C	T	1.041e^-4	0.935	INTRON CG34449
3R	798536	3R_798536_SNP [dm3] 3R_4972814_SNP [dm6]	A	G	1.066e^-4	0.935	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_ttk
2R	10286773	2R_10286773_INS [dm3] 2R_14399268_INS [dm6]	T	TTT	1.086e^-4	0.935	INTERGENIC
3L	19120397	3L_19120397_SNP [dm3] 3L_19127297_SNP [dm6]	T	A	1.117e^-4	0.935	INTRON CG14082	TF binding site mE1_TFBS_inv
3R	13768080	3R_13768080_SNP [dm3] 3R_17942358_SNP [dm6]	G	A	1.121e^-4	0.935	INTRON cpo	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	11178081	3L_11178081_SNP [dm3] 3L_11184981_SNP [dm6]	G	A	1.132e^-4	0.935	INTRON GlcAT-P
2R	16073366	2R_16073366_SNP [dm3] 2R_20185861_SNP [dm6]	C	G	1.157e^-4	0.935	INTERGENIC
3L	22974919	3L_22974919_SNP [dm3] 3L_22981819_SNP [dm6]	T	C	1.180e^-4	0.935	INTERGENIC
2R	10096291	2R_10096291_SNP [dm3] 2R_14208786_SNP [dm6]	T	C	1.192e^-4	0.935	INTRON Sox15	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13250274	3L_13250274_SNP [dm3] 3L_13257174_SNP [dm6]	T	A	1.199e^-4	0.935	INTRON caps
X	19015279	X_19015279_SNP [dm3] X_19121246_SNP [dm6]	G	T	1.222e^-4	0.935	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3L	11756252	3L_11756252_SNP [dm3] 3L_11763152_SNP [dm6]	G	A	1.224e^-4	0.935	INTRON CG6024
X	12425281	X_12425281_SNP [dm3] X_12531248_SNP [dm6]	C	T	1.234e^-4	0.935	UPSTREAM CG43921 INTRON CG43921
X	12425305	X_12425305_SNP [dm3] X_12531272_SNP [dm6]	A	G	1.234e^-4	0.935	UPSTREAM CG43921 INTRON CG43921
3L	21349217	3L_21349217_SNP [dm3] 3L_21356117_SNP [dm6]	G	C	1.266e^-4	0.935	INTRON CG12971
3L	8899337	3L_8899337_SNP [dm3] 3L_8906237_SNP [dm6]	C	T	1.285e^-4	0.935	INTRON mfr
3L	6361188	3L_6361188_SNP [dm3] 3L_6368088_SNP [dm6]	T	C	1.288e^-4	0.935	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
3L	16823477	3L_16823477_SNP [dm3] 3L_16830377_SNP [dm6]	C	G	1.295e^-4	0.935	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	8163686	3L_8163686_SNP [dm3] 3L_8170586_SNP [dm6]	A	C	1.330e^-4	0.935	DOWNSTREAM RecQ4 INTERGENIC	TF binding site mE1_TFBS_cnc
3L	8163697	3L_8163697_SNP [dm3] 3L_8170597_SNP [dm6]	T	A	1.330e^-4	0.935	DOWNSTREAM RecQ4 INTERGENIC	TF binding site mE1_TFBS_cnc
2L	2924944	2L_2924944_SNP [dm3] 2L_2924944_SNP [dm6]	A	G	1.339e^-4	0.935	UTR_5_PRIME lilli INTRON lilli
2R	8898268	2R_8898268_SNP [dm3] 2R_13010763_SNP [dm6]	C	T	1.352e^-4	0.935	INTERGENIC
2R	4936249	2R_4936249_SNP [dm3] 2R_9048744_SNP [dm6]	G	A	1.365e^-4	0.935	INTRON CG13743	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	16794573	2R_16794573_SNP [dm3] 2R_20907068_SNP [dm6]	G	A	1.383e^-4	0.935	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2L	6681395	2L_6681395_INS [dm3] 2L_6681395_INS [dm6]	G	GG	1.396e^-4	0.935	SPLICE_SITE_REGION Nhe3 INTRON Nhe3	TF binding site mE1_TFBS_inv
2R	3091913	2R_3091913_SNP [dm3] 2R_7204408_SNP [dm6]	A	G	1.421e^-4	0.935	INTRON pk
3L	11679686	3L_11679686_SNP [dm3] 3L_11686586_SNP [dm6]	G	C	1.426e^-4	0.935	INTRON Sug
3L	11679696	3L_11679696_SNP [dm3] 3L_11686596_SNP [dm6]	T	A	1.426e^-4	0.935	INTRON Sug
2L	2925096	2L_2925096_SNP [dm3] 2L_2925096_SNP [dm6]	C	T	1.431e^-4	0.935	START_GAINED lilli UTR_5_PRIME lilli INTRON lilli
2R	8898282	2R_8898282_SNP [dm3] 2R_13010777_SNP [dm6]	T	A	1.442e^-4	0.935	INTERGENIC
2R	8898285	2R_8898285_SNP [dm3] 2R_13010780_SNP [dm6]	T	C	1.442e^-4	0.935	INTERGENIC
3R	18795593	3R_18795593_SNP [dm3] 3R_22969871_SNP [dm6]	T	A	1.456e^-4	0.935	INTERGENIC
2R	5399269	2R_5399269_SNP [dm3] 2R_9511764_SNP [dm6]	C	A	1.483e^-4	0.935	INTRON brp
2R	5399270	2R_5399270_SNP [dm3] 2R_9511765_SNP [dm6]	A	C	1.483e^-4	0.935	INTRON brp
3L	13886163	3L_13886163_SNP [dm3] 3L_13893063_SNP [dm6]	A	C	1.485e^-4	0.935	INTRON dysc
3L	13886167	3L_13886167_SNP [dm3] 3L_13893067_SNP [dm6]	G	A	1.485e^-4	0.935	INTRON dysc
2R	10286824	2R_10286824_SNP [dm3] 2R_14399319_SNP [dm6]	C	G	1.492e^-4	0.935	INTERGENIC
3L	6359446	3L_6359446_SNP [dm3] 3L_6366346_SNP [dm6]	T	A	1.493e^-4	0.935	INTERGENIC
2L	10995633	2L_10995633_SNP [dm3] 2L_10995633_SNP [dm6]	C	T	1.494e^-4	0.935	UTR_3_PRIME CG16833 DOWNSTREAM CG16833 INTRON CG16833
3L	11681204	3L_11681204_SNP [dm3] 3L_11688104_SNP [dm6]	A	T	1.496e^-4	0.935	INTRON Sug
3L	11677393	3L_11677393_SNP [dm3] 3L_11684293_SNP [dm6]	A	T	1.513e^-4	0.935	START_GAINED Sug UTR_5_PRIME Sug DOWNSTREAM TfIIEalpha	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	1405874	2R_1405874_SNP [dm3] 2R_5518369_SNP [dm6]	T	C	1.534e^-4	0.935	UPSTREAM CG30438 INTRON CG30438	transposable element FlyBase
3L	11756235	3L_11756235_INS [dm3] 3L_11763135_INS [dm6]	A	AGGATATAAA	1.536e^-4	0.935	INTRON CG6024
2R	8898286	2R_8898286_SNP [dm3] 2R_13010781_SNP [dm6]	C	A	1.558e^-4	0.935	INTERGENIC
3R	27068250	3R_27068250_SNP [dm3] 3R_31242528_SNP [dm6]	T	A	1.562e^-4	0.935	INTRON qless
2R	18287811	2R_18287811_SNP [dm3] 2R_22400306_SNP [dm6]	C	G	1.568e^-4	0.935	INTRON babos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

pupae3 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results