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=2.243e^-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

Covariate	p-value	Significance
wolba	0.03518
In_2L_t	0.07011
In_3R_K	2.493e-15

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.912	0.0858

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2045 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	16921446	3L_16921446_SNP [dm3] 3L_16928346_SNP [dm6]	T	A	2.445e^-6	0.802	UPSTREAM CG13023 DOWNSTREAM CG11905 INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	16391977	2L_16391977_SNP [dm3] 2L_16391977_SNP [dm6]	C	T	2.797e^-6	0.802	INTERGENIC
2R	4171166	2R_4171166_INS [dm3] 2R_8283661_INS [dm6]	C	CCTTTCCGC	3.930e^-6	0.802	INTERGENIC
3R	8388339	3R_8388339_INS [dm3] 3R_12562617_INS [dm6]	C	CA	4.383e^-6	0.802	UTR_5_PRIME Octbeta2R INTRON Octbeta2R
2R	9411448	2R_9411448_SNP [dm3] 2R_13523943_SNP [dm6]	A	G	4.903e^-6	0.802	DOWNSTREAM CG13331 INTRON Vmat
2R	4328782	2R_4328782_SNP [dm3] 2R_8441277_SNP [dm6]	G	A	5.732e^-6	0.802	UPSTREAM Cyp4ad1 INTRON Cyp4ad1
3R	12502464	3R_12502464_SNP [dm3] 3R_16676742_SNP [dm6]	T	C	5.872e^-6	0.802	INTRON Ubx	TF binding site mE1_TFBS_cad
2R	7514709	2R_7514709_SNP [dm3] 2R_11627204_SNP [dm6]	A	C	6.914e^-6	0.802	INTRON CG9005	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	11649434	3L_11649434_SNP [dm3] 3L_11656334_SNP [dm6]	T	G	7.040e^-6	0.802	UPSTREAM mir-274 INTRON CG32085
X	5889450	X_5889450_SNP [dm3] X_5995417_SNP [dm6]	A	G	9.193e^-6	0.802	INTERGENIC
2L	6554945	2L_6554945_SNP [dm3] 2L_6554945_SNP [dm6]	T	C	9.798e^-6	0.802	DOWNSTREAM Osm6 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	10873786	3L_10873786_SNP [dm3] 3L_10880686_SNP [dm6]	G	A	1.016e^-5	0.802	DOWNSTREAM CG6409 & 1 other INTERGENIC	TF binding site mE1_TFBS_chinmo
2R	7514673	2R_7514673_SNP [dm3] 2R_11627168_SNP [dm6]	T	G	1.040e^-5	0.802	INTRON CG9005	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	13096277	3L_13096277_SNP [dm3] 3L_13103177_SNP [dm6]	A	C	1.057e^-5	0.802	INTERGENIC
X	19573525	X_19573525_SNP [dm3] X_19679492_SNP [dm6]	G	A	1.095e^-5	0.802	INTRON dome
3L	17226287	3L_17226287_DEL [dm3] 3L_17233187_DEL [dm6]	TTCTCAAAAT	T	1.107e^-5	0.802	INTRON Rbp6
3L	10896539	3L_10896539_SNP [dm3] 3L_10903439_SNP [dm6]	A	G	1.124e^-5	0.802	INTERGENIC
2R	16966430	2R_16966430_SNP [dm3] 2R_21078925_SNP [dm6]	C	T	1.171e^-5	0.802	INTRON Treh
3R	4038473	3R_4038473_SNP [dm3] 3R_8212751_SNP [dm6]	C	T	1.236e^-5	0.802	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	7514674	2R_7514674_SNP [dm3] 2R_11627169_SNP [dm6]	G	C	1.285e^-5	0.802	INTRON CG9005	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	11936463	3R_11936463_SNP [dm3] 3R_16110741_SNP [dm6]	G	C	1.292e^-5	0.802	INTERGENIC
2R	2587010	2R_2587010_SNP [dm3] 2R_6699505_SNP [dm6]	T	G	1.296e^-5	0.802	DOWNSTREAM CG3409 & 2 others INTERGENIC
3R	4053443	3R_4053443_SNP [dm3] 3R_8227721_SNP [dm6]	G	C	1.305e^-5	0.802	UPSTREAM CR45550 EXON CR45551
3L	21198647	3L_21198647_SNP [dm3] 3L_21205547_SNP [dm6]	A	C	1.356e^-5	0.802	UPSTREAM CG10512 INTRON CG10512	TF binding site mE1_TFBS_cad
2R	3736084	2R_3736084_SNP [dm3] 2R_7848579_SNP [dm6]	G	A	1.390e^-5	0.802	INTRON Dgk
3R	11936481	3R_11936481_DEL [dm3] 3R_16110759_DEL [dm6]	TGGTAT	T	1.419e^-5	0.802	INTERGENIC
2L	15125265	2L_15125265_SNP [dm3] 2L_15125265_SNP [dm6]	A	G	1.479e^-5	0.802	INTERGENIC
2L	11823157	2L_11823157_SNP [dm3] 2L_11823157_SNP [dm6]	G	C	1.485e^-5	0.802	INTRON Pde1c
3R	16411404	3R_16411404_SNP [dm3] 3R_20585682_SNP [dm6]	C	G	1.525e^-5	0.802	UTR_5_PRIME CG16953 DOWNSTREAM Sep2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	7514656	2R_7514656_SNP [dm3] 2R_11627151_SNP [dm6]	C	A	1.559e^-5	0.802	INTRON CG9005	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	13790164	3R_13790164_SNP [dm3] 3R_17964442_SNP [dm6]	T	A	1.636e^-5	0.802	INTRON cpo
3R	11936519	3R_11936519_SNP [dm3] 3R_16110797_SNP [dm6]	T	C	1.674e^-5	0.802	INTERGENIC
3L	10898012	3L_10898012_SNP [dm3] 3L_10904912_SNP [dm6]	G	A	1.692e^-5	0.802	INTERGENIC
2R	15586077	2R_15586077_SNP [dm3] 2R_19698572_SNP [dm6]	T	G	1.795e^-5	0.802	DOWNSTREAM Obp56b & 1 other INTERGENIC
3L	1769452	3L_1769452_SNP [dm3] 3L_1769452_SNP [dm6]	A	C	1.883e^-5	0.802	SYNONYMOUS_CODING Dhc62B	TF binding site mE1_TFBS_cad
3R	26122939	3R_26122939_SNP [dm3] 3R_30297217_SNP [dm6]	T	C	1.930e^-5	0.802	INTRON hdc	TF binding site mE1_TFBS_inv
3L	11649446	3L_11649446_SNP [dm3] 3L_11656346_SNP [dm6]	C	A	1.957e^-5	0.802	UPSTREAM mir-274 INTRON CG32085
X	9264454	X_9264454_SNP [dm3] X_9370421_SNP [dm6]	G	A	1.982e^-5	0.802	SYNONYMOUS_CODING mgl	TF binding site BDTNP1_TFBS_da mE1_TFBS_sens
2L	17932013	2L_17932013_SNP [dm3] 2L_17932013_SNP [dm6]	C	T	2.048e^-5	0.802	INTERGENIC
2R	6460832	2R_6460832_SNP [dm3] 2R_10573327_SNP [dm6]	G	A	2.071e^-5	0.802	INTRON psq
2R	8231748	2R_8231748_SNP [dm3] 2R_12344243_SNP [dm6]	G	T	2.107e^-5	0.802	UPSTREAM ana3 INTRON CG8839	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_ttk
3R	26122931	3R_26122931_SNP [dm3] 3R_30297209_SNP [dm6]	C	A	2.121e^-5	0.802	INTRON hdc	TF binding site mE1_TFBS_inv
2R	3735725	2R_3735725_SNP [dm3] 2R_7848220_SNP [dm6]	G	A	2.122e^-5	0.802	UPSTREAM Dgk INTRON Dgk
2L	18173806	2L_18173806_SNP [dm3] 2L_18173806_SNP [dm6]	C	A	2.180e^-5	0.802	INTRON CG42750
3R	11936475	3R_11936475_SNP [dm3] 3R_16110753_SNP [dm6]	A	C	2.292e^-5	0.802	INTERGENIC
3R	18831372	3R_18831372_SNP [dm3] 3R_23005650_SNP [dm6]	C	G	2.347e^-5	0.802	INTRON CG34375
3R	18867028	3R_18867028_SNP [dm3] 3R_23041306_SNP [dm6]	C	T	2.362e^-5	0.802	UPSTREAM CG13838 EXON CR44226	TF binding site BDTNP1_TFBS_twi
3L	1769458	3L_1769458_SNP [dm3] 3L_1769458_SNP [dm6]	C	T	2.439e^-5	0.802	SYNONYMOUS_CODING Dhc62B	TF binding site mE1_TFBS_cad
2R	2590666	2R_2590666_SNP [dm3] 2R_6703161_SNP [dm6]	G	A	2.450e^-5	0.802	SYNONYMOUS_CODING CG3409 UTR_3_PRIME CG45092	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22827055	3R_22827055_SNP [dm3] 3R_27001333_SNP [dm6]	T	C	2.458e^-5	0.802	SYNONYMOUS_CODING CG31077 INTRON RYa-R	TF binding site mE1_TFBS_sens
3L	12091216	3L_12091216_SNP [dm3] 3L_12098116_SNP [dm6]	C	T	2.463e^-5	0.802	INTERGENIC
3R	22826935	3R_22826935_SNP [dm3] 3R_27001213_SNP [dm6]	C	T	2.486e^-5	0.802	SYNONYMOUS_CODING CG31077 INTRON RYa-R	TF binding site mE1_TFBS_sens
3R	18831378	3R_18831378_SNP [dm3] 3R_23005656_SNP [dm6]	C	A	2.517e^-5	0.802	INTRON CG34375
3R	18814141	3R_18814141_SNP [dm3] 3R_22988419_SNP [dm6]	C	T	2.526e^-5	0.802	SYNONYMOUS_CODING Or94a UPSTREAM Or94b INTRON Nha2
2L	6554939	2L_6554939_SNP [dm3] 2L_6554939_SNP [dm6]	T	A	2.529e^-5	0.802	DOWNSTREAM Osm6 INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	26122967	3R_26122967_SNP [dm3] 3R_30297245_SNP [dm6]	A	T	2.609e^-5	0.802	INTRON hdc	TF binding site mE1_TFBS_inv
X	4339560	X_4339560_SNP [dm3] X_4445527_SNP [dm6]	C	T	2.633e^-5	0.802	INTRON CR32773 & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3L	5478837	3L_5478837_SNP [dm3] 3L_5485737_SNP [dm6]	G	A	2.633e^-5	0.802	INTERGENIC
3L	10890602	3L_10890602_SNP [dm3] 3L_10897502_SNP [dm6]	C	A	2.670e^-5	0.802	INTRON Aps
3L	21800536	3L_21800536_SNP [dm3] 3L_21807436_SNP [dm6]	T	G	2.761e^-5	0.802	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	9032665	2R_9032665_SNP [dm3] 2R_13145160_SNP [dm6]	G	T	2.787e^-5	0.802	UTR_3_PRIME Ack-like INTRON Ack-like
3L	21815445	3L_21815445_SNP [dm3] 3L_21822345_SNP [dm6]	A	C	2.928e^-5	0.802	INTRON CycH	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
X	20024190	X_20024190_SNP [dm3] X_20130157_SNP [dm6]	C	A	2.993e^-5	0.802	DOWNSTREAM CG42582 INTERGENIC
3L	13096384	3L_13096384_SNP [dm3] 3L_13103284_SNP [dm6]	G	A	2.994e^-5	0.802	INTERGENIC
2L	18874715	2L_18874715_SNP [dm3] 2L_18874715_SNP [dm6]	T	G	3.030e^-5	0.802	INTRON tup	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	11649526	3L_11649526_SNP [dm3] 3L_11656426_SNP [dm6]	T	G	3.145e^-5	0.802	UPSTREAM mir-274 INTRON CG32085
2R	3266876	2R_3266876_SNP [dm3] 2R_7379371_SNP [dm6]	C	T	3.151e^-5	0.802	INTRON Dscam1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
2L	16391986	2L_16391986_SNP [dm3] 2L_16391986_SNP [dm6]	C	A	3.155e^-5	0.802	INTERGENIC
3L	11816251	3L_11816251_SNP [dm3] 3L_11823151_SNP [dm6]	C	T	3.165e^-5	0.802	UPSTREAM CG11597 & 1 other DOWNSTREAM snoRNA:Psi18S-920 INTRON RpL10Ab	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	11816253	3L_11816253_SNP [dm3] 3L_11823153_SNP [dm6]	G	A	3.165e^-5	0.802	UPSTREAM CG11597 & 1 other DOWNSTREAM snoRNA:Psi18S-920 INTRON RpL10Ab	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	11816269	3L_11816269_SNP [dm3] 3L_11823169_SNP [dm6]	C	T	3.165e^-5	0.802	UPSTREAM CG11597 & 1 other DOWNSTREAM snoRNA:Psi18S-920 INTRON RpL10Ab	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	11816279	3L_11816279_SNP [dm3] 3L_11823179_SNP [dm6]	A	T	3.165e^-5	0.802	UPSTREAM CG11597 & 1 other DOWNSTREAM snoRNA:Psi18S-920 INTRON RpL10Ab	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	11816705	3L_11816705_SNP [dm3] 3L_11823605_SNP [dm6]	T	C	3.165e^-5	0.802	DOWNSTREAM snoRNA:Psi18S-920 & 1 other INTRON RpL10Ab	TF binding site mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3L	11818414	3L_11818414_SNP [dm3] 3L_11825314_SNP [dm6]	A	T	3.165e^-5	0.802	NON_SYNONYMOUS_CODING CG32095	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	3604441	X_3604441_SNP [dm3] X_3710408_SNP [dm6]	G	A	3.361e^-5	0.831	INTRON Rala
2L	5417954	2L_5417954_SNP [dm3] 2L_5417954_SNP [dm6]	A	T	3.410e^-5	0.831	INTERGENIC
2L	5417960	2L_5417960_SNP [dm3] 2L_5417960_SNP [dm6]	G	A	3.410e^-5	0.831	INTERGENIC
2R	823101	2R_823101_SNP [dm3] 2R_4935596_SNP [dm6]	T	G	3.532e^-5	0.842	INTRON Ir41a	transposable element FlyBase
2L	4012804	2L_4012804_SNP [dm3] 2L_4012804_SNP [dm6]	A	G	3.601e^-5	0.842	INTERGENIC
2R	16967741	2R_16967741_SNP [dm3] 2R_21080236_SNP [dm6]	T	C	3.656e^-5	0.842	UPSTREAM Treh INTRON Treh
3L	11649522	3L_11649522_SNP [dm3] 3L_11656422_SNP [dm6]	G	A	3.681e^-5	0.842	UPSTREAM mir-274 INTRON CG32085
2R	9496921	2R_9496921_SNP [dm3] 2R_13609416_SNP [dm6]	T	C	3.845e^-5	0.842	UPSTREAM CG12464 INTERGENIC
3R	4056534	3R_4056534_SNP [dm3] 3R_8230812_SNP [dm6]	C	T	3.874e^-5	0.842	EXON CR45551
2R	3614489	2R_3614489_SNP [dm3] 2R_7726984_SNP [dm6]	G	A	3.883e^-5	0.842	UPSTREAM CG18812 INTRON CG18812
2R	19372741	2R_19372741_SNP [dm3] 2R_23485218_SNP [dm6]	G	A	3.884e^-5	0.842	SYNONYMOUS_CODING CG43795
2R	10461458	2R_10461458_SNP [dm3] 2R_14573953_SNP [dm6]	A	T	3.899e^-5	0.842	INTRON ttv & 1 other
2R	9579348	2R_9579348_SNP [dm3] 2R_13691843_SNP [dm6]	T	A	3.907e^-5	0.842	UTR_3_PRIME CG6220 INTRON fas
2R	7514748	2R_7514748_INS [dm3] 2R_11627243_INS [dm6]	A	AAGTTAA	4.044e^-5	0.86	INTRON CG9005	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	13128300	3L_13128300_SNP [dm3] 3L_13135200_SNP [dm6]	T	A	4.080e^-5	0.86	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3L	21037364	3L_21037364_SNP [dm3] 3L_21044264_SNP [dm6]	A	G	4.291e^-5	0.894	INTRON siz	TF binding site mE1_TFBS_sens
3R	19126708	3R_19126708_SNP [dm3] 3R_23300986_SNP [dm6]	A	G	4.380e^-5	0.897	INTRON pnt	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	11802520	3L_11802520_SNP [dm3] 3L_11809420_SNP [dm6]	A	T	4.437e^-5	0.897	NON_SYNONYMOUS_CODING CG42255	TF binding site mE1_TFBS_cad
3R	19126717	3R_19126717_SNP [dm3] 3R_23300995_SNP [dm6]	T	C	4.450e^-5	0.897	INTRON pnt	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	17692746	2L_17692746_SNP [dm3] 2L_17692746_SNP [dm6]	G	C	4.547e^-5	0.903	INTRON CadN
3R	4144730	3R_4144730_SNP [dm3] 3R_8319008_SNP [dm6]	A	T	4.642e^-5	0.903	UTR_3_PRIME Ctr1B DOWNSTREAM Poxm
3R	4056610	3R_4056610_SNP [dm3] 3R_8230888_SNP [dm6]	G	A	4.676e^-5	0.903	EXON CR45551
3L	11807447	3L_11807447_SNP [dm3] 3L_11814347_SNP [dm6]	C	G	4.854e^-5	0.903	NON_SYNONYMOUS_CODING CG42255
2R	8166810	2R_8166810_SNP [dm3] 2R_12279305_SNP [dm6]	A	T	4.974e^-5	0.903	UPSTREAM CG42700 DOWNSTREAM Cam INTERGENIC
2R	1344020	2R_1344020_SNP [dm3] 2R_5456515_SNP [dm6]	T	A	4.976e^-5	0.903	DOWNSTREAM laccase2 INTERGENIC	transposable element FlyBase
2L	13873649	2L_13873649_SNP [dm3] 2L_13873649_SNP [dm6]	G	T	5.061e^-5	0.903	INTRON CenG1A

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By genomic position
Variant impact
Gene name

grp phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results