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=1.143e^-15)
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	0.0794086

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.4947	0.0641
In_3R_Mo	5.5514	0.0623

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2294 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	14615289	3R_14615289_SNP [dm3] 3R_18789567_SNP [dm6]	G	A	2.733e^-8	0.036	INTRON CG7720	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	4523264	3L_4523264_SNP [dm3] 3L_4523264_SNP [dm6]	T	C	3.864e^-8	0.036	INTRON Tie	TF binding site mE1_TFBS_inv
3R	12378896	3R_12378896_SNP [dm3] 3R_16553174_SNP [dm6]	G	C	7.728e^-8	0.041	INTRON CG42342	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14117301	3R_14117301_SNP [dm3] 3R_18291579_SNP [dm6]	G	A	1.174e^-7	0.041	INTRON l_3_05822	TF binding site mE1_TFBS_chinmo
3L	4642439	3L_4642439_SNP [dm3] 3L_4642439_SNP [dm6]	T	C	1.269e^-7	0.041	UTR_3_PRIME axo INTRON axo
3R	12378878	3R_12378878_SNP [dm3] 3R_16553156_SNP [dm6]	A	C	1.308e^-7	0.041	INTRON CG42342	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	899116	X_899116_SNP [dm3] X_1005083_SNP [dm6]	T	C	2.191e^-7	0.059	INTERGENIC
3L	12511947	3L_12511947_SNP [dm3] 3L_12518847_SNP [dm6]	A	C	1.099e^-6	0.192	SYNONYMOUS_CODING tral	TF binding site mE1_TFBS_HSA
3L	4642569	3L_4642569_SNP [dm3] 3L_4642569_SNP [dm6]	T	A	1.205e^-6	0.192	UTR_3_PRIME axo INTRON axo
2L	8044259	2L_8044259_SNP [dm3] 2L_8044259_SNP [dm6]	A	T	1.218e^-6	0.192	INTRON CG7466	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	21750825	3L_21750825_SNP [dm3] 3L_21757725_SNP [dm6]	G	A	1.220e^-6	0.192	NON_SYNONYMOUS_CODING CG14564 INTRON Syn1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	9916372	2L_9916372_SNP [dm3] 2L_9916372_SNP [dm6]	C	T	1.233e^-6	0.192	SYNONYMOUS_CODING yip2 DOWNSTREAM CG5885
3R	23892129	3R_23892129_SNP [dm3] 3R_28066407_SNP [dm6]	C	A	1.382e^-6	0.192	INTRON CG34362
2L	7894640	2L_7894640_SNP [dm3] 2L_7894640_SNP [dm6]	A	C	1.433e^-6	0.192	NON_SYNONYMOUS_CODING Snoo	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	9916456	2L_9916456_SNP [dm3] 2L_9916456_SNP [dm6]	G	A	1.907e^-6	0.218	SYNONYMOUS_CODING yip2 DOWNSTREAM CG5885	TF binding site mE1_TFBS_chinmo
2L	8403335	2L_8403335_SNP [dm3] 2L_8403335_SNP [dm6]	G	T	1.977e^-6	0.218	UPSTREAM emb & 1 other DOWNSTREAM CR44991 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA
3R	18165023	3R_18165023_SNP [dm3] 3R_22339301_SNP [dm6]	G	A	1.997e^-6	0.218	INTRON CG5388
X	7645257	X_7645257_SNP [dm3] X_7751224_SNP [dm6]	A	G	2.296e^-6	0.218	INTERGENIC
2R	12244348	2R_12244348_SNP [dm3] 2R_16356843_SNP [dm6]	C	A	2.318e^-6	0.218	UPSTREAM CR43416 INTERGENIC
3L	8047950	3L_8047950_SNP [dm3] 3L_8054850_SNP [dm6]	G	A	2.329e^-6	0.218	NON_SYNONYMOUS_CODING bip1 DOWNSTREAM nmo	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	14098817	3L_14098817_SNP [dm3] 3L_14105717_SNP [dm6]	G	T	2.506e^-6	0.218	INTRON Sox21a	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
3L	4642917	3L_4642917_SNP [dm3] 3L_4642917_SNP [dm6]	T	G	2.559e^-6	0.218	INTRON axo	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo mE1_TFBS_HSA
X	17216280	X_17216280_SNP [dm3] X_17322247_SNP [dm6]	C	A	2.727e^-6	0.222	INTRON B-H2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cnc mE1_TFBS_HSA
3L	4642656	3L_4642656_SNP [dm3] 3L_4642656_SNP [dm6]	A	G	3.378e^-6	0.262	SYNONYMOUS_CODING axo INTRON axo
3L	21696202	3L_21696202_SNP [dm3] 3L_21703102_SNP [dm6]	C	T	3.642e^-6	0.262	INTRON CG32447
X	7646092	X_7646092_SNP [dm3] X_7752059_SNP [dm6]	A	C	4.058e^-6	0.262	INTERGENIC
3L	5246814	3L_5246814_SNP [dm3] 3L_5253714_SNP [dm6]	T	A	4.076e^-6	0.262	INTRON shep
X	3443400	X_3443400_SNP [dm3] X_3549367_SNP [dm6]	A	T	4.136e^-6	0.262	INTRON CG32791
2R	18841344	2R_18841344_SNP [dm3] 2R_22953821_SNP [dm6]	T	A	4.206e^-6	0.262	UPSTREAM CR32835 INTERGENIC
2R	19203065	2R_19203065_SNP [dm3] 2R_23315542_SNP [dm6]	A	C	4.457e^-6	0.262	INTERGENIC
2R	12244327	2R_12244327_SNP [dm3] 2R_16356822_SNP [dm6]	A	T	4.481e^-6	0.262	UPSTREAM CR43416 INTERGENIC
3L	9300002	3L_9300002_SNP [dm3] 3L_9306902_SNP [dm6]	A	T	4.582e^-6	0.262	INTERGENIC
3R	4702424	3R_4702424_SNP [dm3] 3R_8876702_SNP [dm6]	A	T	4.633e^-6	0.262	INTRON pyd
2L	12371978	2L_12371978_SNP [dm3] 2L_12371978_SNP [dm6]	G	C	4.875e^-6	0.262	INTRON bru-2
3R	12379069	3R_12379069_SNP [dm3] 3R_16553347_SNP [dm6]	A	G	4.967e^-6	0.262	INTRON CG42342	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1
2L	7894835	2L_7894835_SNP [dm3] 2L_7894835_SNP [dm6]	C	T	5.031e^-6	0.262	SYNONYMOUS_CODING Snoo	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8583365	2L_8583365_SNP [dm3] 2L_8583365_SNP [dm6]	G	C	5.463e^-6	0.277	INTRON Sema-1a
X	5870289	X_5870289_SNP [dm3] X_5976256_SNP [dm6]	T	C	5.891e^-6	0.278	INTRON Grip
2R	1407715	2R_1407715_SNP [dm3] 2R_5520210_SNP [dm6]	C	T	5.945e^-6	0.278	INTRON CG30438	transposable element FlyBase
X	7645258	X_7645258_SNP [dm3] X_7751225_SNP [dm6]	G	T	6.121e^-6	0.278	INTERGENIC
3L	1084790	3L_1084790_SNP [dm3] 3L_1084790_SNP [dm6]	A	C	6.467e^-6	0.278	INTRON bab1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	7433363	3L_7433363_SNP [dm3] 3L_7440263_SNP [dm6]	T	A	6.497e^-6	0.278	SYNONYMOUS_CODING sphinx2 UPSTREAM sphinx1 INTRON CG42458	TF binding site mE1_TFBS_sens
3L	21728219	3L_21728219_SNP [dm3] 3L_21735119_SNP [dm6]	G	A	6.529e^-6	0.278	UPSTREAM CR43888 DOWNSTREAM CG14573 INTERGENIC
X	7645286	X_7645286_SNP [dm3] X_7751253_SNP [dm6]	T	G	6.568e^-6	0.278	INTERGENIC
3L	7524443	3L_7524443_MNP [dm3] 3L_7531343_MNP [dm6]	TCA	AAT	6.884e^-6	0.278	INTRON lqf
3L	4003814	3L_4003814_SNP [dm3] 3L_4003814_SNP [dm6]	T	A	7.109e^-6	0.278	NON_SYNONYMOUS_CODING CG14985	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	14394135	X_14394135_INS [dm3] X_14500102_INS [dm6]	T	TTCATTATTTT...	7.164e^-6	0.278	INTERGENIC
3L	7524402	3L_7524402_SNP [dm3] 3L_7531302_SNP [dm6]	C	T	7.352e^-6	0.278	INTRON lqf
2L	7016878	2L_7016878_SNP [dm3] 2L_7016878_SNP [dm6]	C	T	7.504e^-6	0.278	NON_SYNONYMOUS_CODING ade3	TF binding site mE1_TFBS_chinmo
2R	17621234	2R_17621234_SNP [dm3] 2R_21733729_SNP [dm6]	C	T	7.786e^-6	0.278	INTERGENIC
2L	8044273	2L_8044273_SNP [dm3] 2L_8044273_SNP [dm6]	C	T	7.850e^-6	0.278	INTRON CG7466	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	1432979	2L_1432979_SNP [dm3] 2L_1432979_SNP [dm6]	C	T	7.870e^-6	0.278	DOWNSTREAM snRNA:U3:22A INTERGENIC
2R	19739627	2R_19739627_SNP [dm3] 2R_23852104_SNP [dm6]	A	C	7.951e^-6	0.278	NON_SYNONYMOUS_CODING gbb UPSTREAM ytr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	17717608	3R_17717608_SNP [dm3] 3R_21891886_SNP [dm6]	A	T	8.055e^-6	0.278	INTRON CG6678	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	19346861	X_19346861_SNP [dm3] X_19452828_SNP [dm6]	G	A	8.223e^-6	0.278	INTRON kek5	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	21696960	3L_21696960_SNP [dm3] 3L_21703860_SNP [dm6]	G	C	8.396e^-6	0.278	INTRON CG32447	TF binding site mE1_TFBS_HSA
3R	9333654	3R_9333654_SNP [dm3] 3R_13507932_SNP [dm6]	C	A	8.587e^-6	0.278	INTERGENIC
3R	10596377	3R_10596377_SNP [dm3] 3R_14770655_SNP [dm6]	T	C	8.642e^-6	0.278	INTRON jvl
3L	21695646	3L_21695646_SNP [dm3] 3L_21702546_SNP [dm6]	A	C	8.981e^-6	0.278	INTRON CG32447
3R	16751627	3R_16751627_SNP [dm3] 3R_20925905_SNP [dm6]	C	G	9.024e^-6	0.278	INTRON CG31191 & 1 other
3R	10159077	3R_10159077_SNP [dm3] 3R_14333355_SNP [dm6]	A	T	9.169e^-6	0.278	INTRON NK7.1
2R	5287568	2R_5287568_DEL [dm3] 2R_9400063_DEL [dm6]	CAC	C	9.187e^-6	0.278	UTR_5_PRIME CG33774 DOWNSTREAM wun & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_inv
2L	9259402	2L_9259402_SNP [dm3] 2L_9259402_SNP [dm6]	C	A	9.485e^-6	0.282	UTR_5_PRIME Ggamma30A INTRON Ggamma30A
3R	3164974	3R_3164974_SNP [dm3] 3R_7339252_SNP [dm6]	C	T	9.735e^-6	0.285	INTERGENIC	TF binding site mE1_TFBS_cad
2L	5461503	2L_5461503_SNP [dm3] 2L_5461503_SNP [dm6]	C	A	1.066e^-5	0.308	UPSTREAM mid INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_eve mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Stat92E mE1_TFBS_Trl mE1_TFBS_Ubx
X	12676864	X_12676864_SNP [dm3] X_12782831_SNP [dm6]	G	A	1.157e^-5	0.329	INTRON CG32647
3L	7524438	3L_7524438_SNP [dm3] 3L_7531338_SNP [dm6]	A	C	1.190e^-5	0.329	INTRON lqf
2R	11765664	2R_11765664_SNP [dm3] 2R_15878159_SNP [dm6]	T	A	1.192e^-5	0.329	INTRON sli
2L	3379601	2L_3379601_SNP [dm3] 2L_3379601_SNP [dm6]	G	A	1.219e^-5	0.331	INTERGENIC
X	917107	X_917107_SNP [dm3] X_1023074_SNP [dm6]	G	A	1.244e^-5	0.333	INTRON su_w[a]_ & 2 others
2R	12246141	2R_12246141_SNP [dm3] 2R_16358636_SNP [dm6]	C	T	1.282e^-5	0.334	DOWNSTREAM CR45322 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA
3L	7524344	3L_7524344_SNP [dm3] 3L_7531244_SNP [dm6]	A	T	1.286e^-5	0.334	INTRON lqf
X	21297532	X_21297532_DEL [dm3] X_21426505_DEL [dm6]	TGTTGCGTAT	T	1.322e^-5	0.334	INTRON CG42343
3R	18867947	3R_18867947_SNP [dm3] 3R_23042225_SNP [dm6]	C	T	1.336e^-5	0.334	UPSTREAM CG13838 DOWNSTREAM CR44226 INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	12094287	2R_12094287_SNP [dm3] 2R_16206782_SNP [dm6]	C	A	1.347e^-5	0.334	UPSTREAM mrj DOWNSTREAM tRNA:CR30237 INTRON mrj	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	11284969	3R_11284969_SNP [dm3] 3R_15459247_SNP [dm6]	C	T	1.355e^-5	0.334	INTRON AdamTS-A
3R	16528826	3R_16528826_SNP [dm3] 3R_20703104_SNP [dm6]	C	G	1.379e^-5	0.336	INTRON Oamb
2R	12246163	2R_12246163_SNP [dm3] 2R_16358658_SNP [dm6]	A	C	1.408e^-5	0.339	DOWNSTREAM CR45322 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA
2L	3385183	2L_3385183_SNP [dm3] 2L_3385183_SNP [dm6]	A	G	1.452e^-5	0.345	INTERGENIC
3L	4642730	3L_4642730_SNP [dm3] 3L_4642730_SNP [dm6]	C	G	1.482e^-5	0.345	NON_SYNONYMOUS_CODING axo	TF binding site mE1_TFBS_chinmo
X	898466	X_898466_SNP [dm3] X_1004433_SNP [dm6]	A	G	1.501e^-5	0.345	INTERGENIC
3L	12942220	3L_12942220_SNP [dm3] 3L_12949120_SNP [dm6]	C	A	1.506e^-5	0.345	INTERGENIC
2R	19739712	2R_19739712_SNP [dm3] 2R_23852189_SNP [dm6]	G	A	1.554e^-5	0.346	SYNONYMOUS_CODING gbb UPSTREAM ytr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	12246176	2R_12246176_DEL [dm3] 2R_16358671_DEL [dm6]	AA	A	1.556e^-5	0.346	DOWNSTREAM CR45322 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA
2L	3385215	2L_3385215_INS [dm3] 2L_3385215_INS [dm6]	GGC	TTTCACAG	1.566e^-5	0.346	INTERGENIC
2L	12407738	2L_12407738_SNP [dm3] 2L_12407738_SNP [dm6]	T	A	1.586e^-5	0.346	SPLICE_SITE_REGION vir-1 INTRON vir-1
X	19722384	X_19722384_INS [dm3] X_19828351_INS [dm6]	A	ACGGTCAGGA	1.627e^-5	0.351	INTERGENIC
2R	19046914	2R_19046914_SNP [dm3] 2R_23159391_SNP [dm6]	G	A	1.666e^-5	0.355	SYNONYMOUS_CODING CG9899
3L	7432891	3L_7432891_INS [dm3] 3L_7439791_INS [dm6]	T	TGAAT	1.734e^-5	0.36	UTR_3_PRIME sphinx2 UPSTREAM sphinx1 INTRON CG42458
3L	21708318	3L_21708318_SNP [dm3] 3L_21715218_SNP [dm6]	G	T	1.771e^-5	0.36	INTERGENIC
2L	5670982	2L_5670982_SNP [dm3] 2L_5670982_SNP [dm6]	T	C	1.776e^-5	0.36	DOWNSTREAM Hsp60C INTERGENIC	TF binding site mE1_TFBS_chinmo
X	5870568	X_5870568_SNP [dm3] X_5976535_SNP [dm6]	C	T	1.783e^-5	0.36	INTRON Grip
2R	11765639	2R_11765639_SNP [dm3] 2R_15878134_SNP [dm6]	A	G	1.785e^-5	0.36	INTRON sli
2R	9290446	2R_9290446_SNP [dm3] 2R_13402941_SNP [dm6]	C	T	1.810e^-5	0.361	INTERGENIC
2L	3374498	2L_3374498_SNP [dm3] 2L_3374498_SNP [dm6]	C	T	1.854e^-5	0.363	SYNONYMOUS_CODING CG15412	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8051124	2L_8051124_SNP [dm3] 2L_8051124_SNP [dm6]	G	C	1.858e^-5	0.363	SYNONYMOUS_CODING CG7466	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12489802	3L_12489802_SNP [dm3] 3L_12496702_SNP [dm6]	G	A	1.922e^-5	0.372	INTRON CG10657
3R	16703869	3R_16703869_SNP [dm3] 3R_20878147_SNP [dm6]	G	A	1.975e^-5	0.373	SYNONYMOUS_CODING TotZ DOWNSTREAM CR44048
3R	23947861	3R_23947861_SNP [dm3] 3R_28122139_SNP [dm6]	T	C	1.991e^-5	0.373	INTERGENIC
3R	8488327	3R_8488327_SNP [dm3] 3R_12662605_SNP [dm6]	G	C	2.000e^-5	0.373	UPSTREAM CG14395 & 1 other INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Survival_Radiation phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results