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=6.890e^-4)
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	4.9116	0.0267

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1449 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	14666075	3R_14666075_SNP [dm3] 3R_18840353_SNP [dm6]	A	C	1.044e^-14	1.706e^-8	INTRON CG18208
3R	16609138	3R_16609138_SNP [dm3] 3R_20783416_SNP [dm6]	A	G	8.941e^-8	0.073	START_GAINED Syp UTR_5_PRIME Syp INTRON Syp	TF binding site BDTNP1_TFBS_dl
X	5072285	X_5072285_SNP [dm3] X_5178252_SNP [dm6]	A	G	3.849e^-6	0.346	INTRON rg & 1 other
2R	10395274	2R_10395274_SNP [dm3] 2R_14507769_SNP [dm6]	G	C	7.930e^-6	0.346	SYNONYMOUS_CODING Asx
2L	18324805	2L_18324805_INS [dm3] 2L_18324805_INS [dm6]	T	TT	8.604e^-6	0.346	INTRON Fas3
3L	16483161	3L_16483161_SNP [dm3] 3L_16490061_SNP [dm6]	C	T	8.604e^-6	0.346	INTRON CG33158	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3R	10128606	3R_10128606_SNP [dm3] 3R_14302884_SNP [dm6]	C	T	8.604e^-6	0.346	SYNONYMOUS_CODING CG3259 DOWNSTREAM CG12207	TF binding site mE1_TFBS_cad
X	8510882	X_8510882_INS [dm3] X_8616849_INS [dm6]	C	CGCCATCTC	9.644e^-6	0.346	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	11090311	2L_11090311_SNP [dm3] 2L_11090311_SNP [dm6]	C	T	1.176e^-5	0.346	SYNONYMOUS_CODING CG16854	TF binding site mE1_TFBS_cad
2L	14490104	2L_14490104_SNP [dm3] 2L_14490104_SNP [dm6]	C	A	1.176e^-5	0.346	UPSTREAM noc INTERGENIC	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_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl
2L	18076104	2L_18076104_SNP [dm3] 2L_18076104_SNP [dm6]	T	C	1.176e^-5	0.346	INTERGENIC
2L	2449385	2L_2449385_SNP [dm3] 2L_2449385_SNP [dm6]	T	A	1.176e^-5	0.346	UPSTREAM dpp INTRON dpp	enhancer FlyBase regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2L	7524119	2L_7524119_SNP [dm3] 2L_7524119_SNP [dm6]	A	T	1.176e^-5	0.346	INTRON RapGAP1
2R	18641095	2R_18641095_SNP [dm3] 2R_22753590_SNP [dm6]	T	A	1.176e^-5	0.346	INTRON CG42260
3L	10621853	3L_10621853_SNP [dm3] 3L_10628753_SNP [dm6]	T	C	1.176e^-5	0.346	UPSTREAM CG14151 DOWNSTREAM CG42536 INTERGENIC	TF binding site mE1_TFBS_inv
3L	1422927	3L_1422927_SNP [dm3] 3L_1422927_SNP [dm6]	C	T	1.176e^-5	0.346	NON_SYNONYMOUS_CODING CG9173 INTRON Ptp61F	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	16495315	3L_16495315_SNP [dm3] 3L_16502215_SNP [dm6]	T	A	1.176e^-5	0.346	UTR_3_PRIME CG43373 INTRON CG43373	TF binding site mE1_TFBS_cad
3L	702755	3L_702755_SNP [dm3] 3L_702755_SNP [dm6]	A	G	1.176e^-5	0.346	INTERGENIC
3R	14466824	3R_14466824_SNP [dm3] 3R_18641102_SNP [dm6]	A	C	1.176e^-5	0.346	START_GAINED CG14301 UTR_5_PRIME CG14301 INTRON qin	TF binding site BDTNP1_TFBS_z
X	3713549	X_3713549_SNP [dm3] X_3819516_SNP [dm6]	G	T	1.176e^-5	0.346	UPSTREAM tRNA:CR32785 INTRON ec
X	3713824	X_3713824_SNP [dm3] X_3819791_SNP [dm6]	G	T	1.176e^-5	0.346	DOWNSTREAM tRNA:CR32785 INTRON ec
X	3713967	X_3713967_SNP [dm3] X_3819934_SNP [dm6]	G	T	1.176e^-5	0.346	DOWNSTREAM tRNA:CR32785 INTRON ec
X	4530241	X_4530241_SNP [dm3] X_4636208_SNP [dm6]	C	A	1.176e^-5	0.346	UPSTREAM pon & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	7266443	2R_7266443_SNP [dm3] 2R_11378938_SNP [dm6]	C	A	2.076e^-5	0.346	INTRON Tsp47F
X	5229614	X_5229614_SNP [dm3] X_5335581_SNP [dm6]	C	T	2.076e^-5	0.346	INTERGENIC
2R	10398312	2R_10398312_SNP [dm3] 2R_14510807_SNP [dm6]	G	C	2.925e^-5	0.346	DOWNSTREAM Asx INTRON Asx
X	8553145	X_8553145_SNP [dm3] X_8659112_SNP [dm6]	A	G	3.263e^-5	0.346	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_slp1 mE1_TFBS_HSA
X	3810232	X_3810232_SNP [dm3] X_3916199_SNP [dm6]	T	C	3.306e^-5	0.346	INTRON CG42541
2L	7675436	2L_7675436_SNP [dm3] 2L_7675436_SNP [dm6]	A	C	4.005e^-5	0.346	UPSTREAM Slob INTRON Myo28B1
3L	10048374	3L_10048374_SNP [dm3] 3L_10055274_SNP [dm6]	C	T	4.367e^-5	0.346	INTRON dpr6
3L	15438496	3L_15438496_SNP [dm3] 3L_15445396_SNP [dm6]	A	C	4.458e^-5	0.346	INTERGENIC
X	18369155	X_18369155_SNP [dm3] X_18475122_SNP [dm6]	C	T	4.458e^-5	0.346	INTRON CG32547
2L	10510089	2L_10510089_SNP [dm3] 2L_10510089_SNP [dm6]	T	C	4.709e^-5	0.346	SYNONYMOUS_CODING CG7384 DOWNSTREAM Fatp & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	1232506	2L_1232506_SNP [dm3] 2L_1232506_SNP [dm6]	C	T	4.709e^-5	0.346	INTERGENIC
2L	13074012	2L_13074012_SNP [dm3] 2L_13074012_SNP [dm6]	C	T	4.709e^-5	0.346	INTERGENIC	TF binding site mE1_TFBS_inv
2L	1365573	2L_1365573_SNP [dm3] 2L_1365573_SNP [dm6]	A	C	4.709e^-5	0.346	INTERGENIC
2L	1691054	2L_1691054_DEL [dm3] 2L_1691054_DEL [dm6]	CATCCCATCGCAC...	C	4.709e^-5	0.346	INTRON chinmo
2L	19240162	2L_19240162_SNP [dm3] 2L_19240162_SNP [dm6]	T	G	4.709e^-5	0.346	INTERGENIC
2L	19979546	2L_19979546_SNP [dm3] 2L_19979546_SNP [dm6]	A	T	4.709e^-5	0.346	INTRON CG43861 EXON CR43620
2L	3674745	2L_3674745_SNP [dm3] 2L_3674745_SNP [dm6]	T	C	4.709e^-5	0.346	INTRON CG34340
2L	5934496	2L_5934496_SNP [dm3] 2L_5934496_SNP [dm6]	A	T	4.709e^-5	0.346	INTRON dsf	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_HSA
2L	7252564	2L_7252564_SNP [dm3] 2L_7252564_SNP [dm6]	C	T	4.709e^-5	0.346	NON_SYNONYMOUS_CODING CG13786
2L	8206272	2L_8206272_SNP [dm3] 2L_8206272_SNP [dm6]	G	T	4.709e^-5	0.346	START_GAINED CG8419 UTR_5_PRIME CG8419 UPSTREAM CR44120 & 1 other DOWNSTREAM CR44119	TF binding site mE1_TFBS_chinmo
2L	9350382	2L_9350382_SNP [dm3] 2L_9350382_SNP [dm6]	A	G	4.709e^-5	0.346	UPSTREAM CG13110 DOWNSTREAM CG43350 INTERGENIC
2R	10963778	2R_10963778_SNP [dm3] 2R_15076273_SNP [dm6]	G	A	4.709e^-5	0.346	INTERGENIC
2R	10963780	2R_10963780_SNP [dm3] 2R_15076275_SNP [dm6]	C	A	4.709e^-5	0.346	INTERGENIC
2R	10963782	2R_10963782_SNP [dm3] 2R_15076277_SNP [dm6]	T	A	4.709e^-5	0.346	INTERGENIC
2R	10963784	2R_10963784_INS [dm3] 2R_15076279_INS [dm6]	A	AGACATA	4.709e^-5	0.346	INTERGENIC
2R	12407370	2R_12407370_SNP [dm3] 2R_16519865_SNP [dm6]	G	A	4.709e^-5	0.346	INTRON Sema-2a	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2R	13175832	2R_13175832_SNP [dm3] 2R_17288327_SNP [dm6]	C	G	4.709e^-5	0.346	INTRON mbl
2R	16223108	2R_16223108_SNP [dm3] 2R_20335603_SNP [dm6]	C	G	4.709e^-5	0.346	INTERGENIC
2R	18156237	2R_18156237_SNP [dm3] 2R_22268732_SNP [dm6]	T	A	4.709e^-5	0.346	INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	1942502	2R_1942502_SNP [dm3] 2R_6054997_SNP [dm6]	G	T	4.709e^-5	0.346	INTRON CCHa2-R	TF binding site mE1_TFBS_sens
3L	17692394	3L_17692394_SNP [dm3] 3L_17699294_SNP [dm6]	G	A	4.709e^-5	0.346	INTRON Ccn
3L	1909918	3L_1909918_SNP [dm3] 3L_1909918_SNP [dm6]	G	A	4.709e^-5	0.346	UTR_5_PRIME CG1887
3L	4180553	3L_4180553_SNP [dm3] 3L_4180553_SNP [dm6]	T	G	4.709e^-5	0.346	INTRON CG18675 & 1 other	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	6180567	3L_6180567_SNP [dm3] 3L_6187467_SNP [dm6]	T	C	4.709e^-5	0.346	SYNONYMOUS_CODING D19A	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	6855101	3L_6855101_SNP [dm3] 3L_6862001_SNP [dm6]	G	A	4.709e^-5	0.346	INTERGENIC
3L	8805340	3L_8805340_SNP [dm3] 3L_8812240_SNP [dm6]	T	A	4.709e^-5	0.346	DOWNSTREAM CG13309 INTERGENIC
3R	11533818	3R_11533818_SNP [dm3] 3R_15708096_SNP [dm6]	C	G	4.709e^-5	0.346	UTR_3_PRIME CG5404	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	23399582	3R_23399582_SNP [dm3] 3R_27573860_SNP [dm6]	A	C	4.709e^-5	0.346	INTRON wdb
3R	8100004	3R_8100004_SNP [dm3] 3R_12274282_SNP [dm6]	G	A	4.709e^-5	0.346	DOWNSTREAM Sfp87B INTRON svp
X	16212482	X_16212482_SNP [dm3] X_16318449_SNP [dm6]	C	T	4.709e^-5	0.346	SYNONYMOUS_CODING Cyp1 DOWNSTREAM CG13957	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
X	18405481	X_18405481_SNP [dm3] X_18511448_SNP [dm6]	C	G	4.709e^-5	0.346	INTRON Ggt-1
X	3360029	X_3360029_SNP [dm3] X_3465996_SNP [dm6]	A	C	4.709e^-5	0.346	UTR_3_PRIME CG12206 INTRON CR44999
X	3552474	X_3552474_SNP [dm3] X_3658441_SNP [dm6]	A	G	4.709e^-5	0.346	INTRON AstA-R1
X	8090061	X_8090061_SNP [dm3] X_8196028_SNP [dm6]	A	T	4.709e^-5	0.346	INTRON sdt	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
X	8710179	X_8710179_SNP [dm3] X_8816146_SNP [dm6]	T	C	4.709e^-5	0.346	INTERGENIC
2L	7554100	2L_7554100_SNP [dm3] 2L_7554100_SNP [dm6]	T	C	5.510e^-5	0.346	INTRON RapGAP1
3R	20730597	3R_20730597_SNP [dm3] 3R_24904875_SNP [dm6]	T	A	6.093e^-5	0.346	INTRON CG13643
3R	20730603	3R_20730603_INS [dm3] 3R_24904881_INS [dm6]	T	TAT	6.093e^-5	0.346	INTRON CG13643
3R	7271234	3R_7271234_SNP [dm3] 3R_11445512_SNP [dm6]	G	T	6.439e^-5	0.346	INTRON CG17230 & 1 other
X	16141732	X_16141732_SNP [dm3] X_16247699_SNP [dm6]	G	T	6.628e^-5	0.346	INTERGENIC
3L	1024185	3L_1024185_INS [dm3] 3L_1024185_INS [dm6]	A	ATCATAAGAGGTAATGATAT...	6.850e^-5	0.346	INTRON trio	TF binding site mE1_TFBS_cad
3L	1118897	3L_1118897_SNP [dm3] 3L_1118897_SNP [dm6]	C	G	6.850e^-5	0.346	INTERGENIC	TF binding site mE1_TFBS_cad
3L	4057641	3L_4057641_SNP [dm3] 3L_4057641_SNP [dm6]	G	A	6.850e^-5	0.346	INTRON CG1136	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	3714699	X_3714699_INS [dm3] X_3820666_INS [dm6]	G	GAG	6.850e^-5	0.346	DOWNSTREAM tRNA:CR32785 INTRON ec	TF binding site mE1_TFBS_HSA
3L	5944595	3L_5944595_SNP [dm3] 3L_5951495_SNP [dm6]	A	C	7.037e^-5	0.346	UPSTREAM CG33993 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	13159219	3R_13159219_SNP [dm3] 3R_17333497_SNP [dm6]	G	T	8.590e^-5	0.346	INTRON beat-IIa	TF binding site BDTNP1_TFBS_dl
3R	17034875	3R_17034875_SNP [dm3] 3R_21209153_SNP [dm6]	A	T	8.590e^-5	0.346	INTRON SNF4Agamma
3L	15318739	3L_15318739_SNP [dm3] 3L_15325639_SNP [dm6]	T	G	1.047e^-4	0.346	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_hkb mE1_TFBS_HSA
3L	15318760	3L_15318760_SNP [dm3] 3L_15325660_SNP [dm6]	A	C	1.047e^-4	0.346	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_hkb mE1_TFBS_HSA
3L	3203388	3L_3203388_SNP [dm3] 3L_3203388_SNP [dm6]	A	C	1.047e^-4	0.346	UPSTREAM CG32271 DOWNSTREAM CG33159 INTRON gry
X	10571706	X_10571706_SNP [dm3] X_10677673_SNP [dm6]	T	G	1.047e^-4	0.346	INTRON X11Lbeta
2R	7266548	2R_7266548_SNP [dm3] 2R_11379043_SNP [dm6]	G	A	1.141e^-4	0.346	UTR_5_PRIME Tsp47F
3R	26001422	3R_26001422_SNP [dm3] 3R_30175700_SNP [dm6]	C	A	1.141e^-4	0.346	DOWNSTREAM CG1983 INTERGENIC	regulatory region REDfly_CRMs
2L	9393510	2L_9393510_SNP [dm3] 2L_9393510_SNP [dm6]	G	T	1.236e^-4	0.346	INTRON Shawl
3R	10329552	3R_10329552_INS [dm3] 3R_14503830_INS [dm6]	A	AT	1.242e^-4	0.346	INTRON CR44177	TF binding site mE1_TFBS_cad
3R	11696176	3R_11696176_DEL [dm3] 3R_15870454_DEL [dm6]	TCTGT	T	1.242e^-4	0.346	INTRON CG31183
3R	17821485	3R_17821485_DEL [dm3] 3R_21995763_DEL [dm6]	AAGA	A	1.242e^-4	0.346
2L	10122683	2L_10122683_SNP [dm3] 2L_10122683_SNP [dm6]	A	C	1.298e^-4	0.346	NON_SYNONYMOUS_CODING CG13135 INTRON CG44153 & 1 other
2L	10568600	2L_10568600_SNP [dm3] 2L_10568600_SNP [dm6]	C	T	1.298e^-4	0.346	DOWNSTREAM CG6138 INTRON Trim9
2L	10569030	2L_10569030_SNP [dm3] 2L_10569030_SNP [dm6]	G	A	1.298e^-4	0.346	INTRON Trim9
2L	10571056	2L_10571056_SNP [dm3] 2L_10571056_SNP [dm6]	C	T	1.298e^-4	0.346	INTRON Trim9
2L	10585705	2L_10585705_SNP [dm3] 2L_10585705_SNP [dm6]	T	C	1.298e^-4	0.346	INTRON Trim9
2L	10586733	2L_10586733_SNP [dm3] 2L_10586733_SNP [dm6]	G	A	1.298e^-4	0.346	INTRON Trim9	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10625354	2L_10625354_SNP [dm3] 2L_10625354_SNP [dm6]	C	T	1.298e^-4	0.346	INTRON Trim9
2L	10681187	2L_10681187_SNP [dm3] 2L_10681187_SNP [dm6]	C	T	1.298e^-4	0.346	SYNONYMOUS_CODING CG17105 UPSTREAM CR44180 & 1 other
2L	1078190	2L_1078190_SNP [dm3] 2L_1078190_SNP [dm6]	C	G	1.298e^-4	0.346	SYNONYMOUS_CODING ast UPSTREAM S	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_sens
2L	10934126	2L_10934126_SNP [dm3] 2L_10934126_SNP [dm6]	A	G	1.298e^-4	0.346	INTRON dpr2

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Age phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results