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=1.534e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_2R_NS	0.01583

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	8.5755	0.0137

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1867 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
X	17014404	X_17014404_SNP [dm3] X_17120371_SNP [dm6]	A	G	6.512e^-7	0.83	INTRON CG5004
2R	16532876	2R_16532876_SNP [dm3] 2R_20645371_SNP [dm6]	G	A	8.859e^-7	0.83	SPLICE_SITE_REGION DMAP1 UPSTREAM Lrt INTRON DMAP1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	10873423	X_10873423_SNP [dm3] X_10979390_SNP [dm6]	T	C	1.819e^-6	0.96	INTRON CG42339
2L	5811554	2L_5811554_DEL [dm3] 2L_5811554_DEL [dm6]	AA	A	3.144e^-6	0.96	UPSTREAM CG43307 DOWNSTREAM CR44576 INTERGENIC
3L	521489	3L_521489_INS [dm3] 3L_521489_INS [dm6]	T	TT	3.833e^-6	0.96	INTRON klar
2R	15385771	2R_15385771_SNP [dm3] 2R_19498266_SNP [dm6]	A	C	5.215e^-6	0.96	SYNONYMOUS_CODING CG15120	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10548553	2L_10548553_SNP [dm3] 2L_10548553_SNP [dm6]	G	A	5.873e^-6	0.96	INTRON Trim9	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_cad mE1_TFBS_HSA
X	18841081	X_18841081_SNP [dm3] X_18947048_SNP [dm6]	C	T	6.129e^-6	0.96	INTRON CG43759	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	12011510	3R_12011510_SNP [dm3] 3R_16185788_SNP [dm6]	T	C	6.983e^-6	0.96	SYNONYMOUS_CODING CG8927 DOWNSTREAM Bin1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	18841099	X_18841099_SNP [dm3] X_18947066_SNP [dm6]	A	G	7.108e^-6	0.96	INTRON CG43759	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	11242370	3R_11242370_SNP [dm3] 3R_15416648_SNP [dm6]	C	T	7.560e^-6	0.96	UTR_3_PRIME Atx2 DOWNSTREAM Atx2 & 2 others
2R	9934186	2R_9934186_SNP [dm3] 2R_14046681_SNP [dm6]	A	G	7.894e^-6	0.96	INTRON mam
X	10873406	X_10873406_SNP [dm3] X_10979373_SNP [dm6]	C	T	8.035e^-6	0.96	INTRON CG42339
3L	19218515	3L_19218515_SNP [dm3] 3L_19225415_SNP [dm6]	T	C	8.845e^-6	0.96	INTRON fz2
2L	12253694	2L_12253694_SNP [dm3] 2L_12253694_SNP [dm6]	C	T	9.808e^-6	0.96	INTRON aret
X	10873320	X_10873320_SNP [dm3] X_10979287_SNP [dm6]	G	C	1.053e^-5	0.96	INTRON CG42339
3R	15919371	3R_15919371_SNP [dm3] 3R_20093649_SNP [dm6]	G	C	1.090e^-5	0.96	INTERGENIC
3L	559571	3L_559571_SNP [dm3] 3L_559571_SNP [dm6]	G	A	1.163e^-5	0.96	INTRON hipk
X	5954122	X_5954122_SNP [dm3] X_6060089_SNP [dm6]	C	A	1.184e^-5	0.96	SYNONYMOUS_CODING CG5921	TF binding site mE1_TFBS_chinmo
2L	8661955	2L_8661955_SNP [dm3] 2L_8661955_SNP [dm6]	A	G	1.501e^-5	0.96	INTRON Sema-1a
2R	6083531	2R_6083531_SNP [dm3] 2R_10196026_SNP [dm6]	G	T	1.539e^-5	0.96	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
3R	13895798	3R_13895798_SNP [dm3] 3R_18070076_SNP [dm6]	G	C	1.596e^-5	0.96	INTERGENIC
X	10873449	X_10873449_SNP [dm3] X_10979416_SNP [dm6]	T	A	1.621e^-5	0.96	INTRON CG42339
3L	9359250	3L_9359250_SNP [dm3] 3L_9366150_SNP [dm6]	G	A	1.696e^-5	0.96	SYNONYMOUS_CODING Klp67A DOWNSTREAM CG4447	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	15895689	2L_15895689_SNP [dm3] 2L_15895689_SNP [dm6]	G	T	1.780e^-5	0.96	UTR_5_PRIME CG31735
X	17007525	X_17007525_MNP [dm3] X_17113492_MNP [dm6]	ACTT	GGCG	1.842e^-5	0.96	INTRON CG5004
X	17007530	X_17007530_INS [dm3] X_17113497_INS [dm6]	T	GC	1.842e^-5	0.96	INTRON CG5004
3L	13332818	3L_13332818_SNP [dm3] 3L_13339718_SNP [dm6]	A	G	1.846e^-5	0.96	INTERGENIC
3L	19669710	3L_19669710_SNP [dm3] 3L_19676610_SNP [dm6]	G	T	1.853e^-5	0.96	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	8101988	2L_8101988_SNP [dm3] 2L_8101988_SNP [dm6]	T	G	1.957e^-5	0.96	INTRON Bsg	TF binding site mE1_TFBS_sbb
3R	7098298	3R_7098298_DEL [dm3] 3R_11272576_DEL [dm6]	TCCTTGGTTTGGGT...	T	2.028e^-5	0.96	INTRON CR31386
2L	5811596	2L_5811596_SNP [dm3] 2L_5811596_SNP [dm6]	C	T	2.029e^-5	0.96	NON_SYNONYMOUS_CODING CG43307 DOWNSTREAM CR44576
X	17007533	X_17007533_MNP [dm3] X_17113500_MNP [dm6]	GCAT	TAGG	2.083e^-5	0.96	INTRON CG5004
X	17007538	X_17007538_SNP [dm3] X_17113505_SNP [dm6]	T	A	2.083e^-5	0.96	INTRON CG5004
2L	12110705	2L_12110705_MNP [dm3] 2L_12110705_MNP [dm6]	ACC	GTT	2.129e^-5	0.96	UPSTREAM Phae2 DOWNSTREAM Phae1 INTERGENIC	TF binding site mE1_TFBS_Trl
3L	13333912	3L_13333912_SNP [dm3] 3L_13340812_SNP [dm6]	G	T	2.148e^-5	0.96	INTERGENIC
X	17007544	X_17007544_INS [dm3] X_17113511_INS [dm6]	T	TT	2.316e^-5	0.96	INTRON CG5004
2R	10527544	2R_10527544_SNP [dm3] 2R_14640039_SNP [dm6]	G	A	2.339e^-5	0.96	DOWNSTREAM CG12862 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
2L	10548570	2L_10548570_SNP [dm3] 2L_10548570_SNP [dm6]	A	G	2.374e^-5	0.96	INTRON Trim9	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_cad mE1_TFBS_HSA
2L	12849679	2L_12849679_INS [dm3] 2L_12849679_INS [dm6]	T	TGCCATT	2.445e^-5	0.96	INTERGENIC
X	4006391	X_4006391_SNP [dm3] X_4112358_SNP [dm6]	T	A	2.544e^-5	0.96	SYNONYMOUS_CODING Nsun2	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	14830590	3L_14830590_SNP [dm3] 3L_14837490_SNP [dm6]	G	A	2.617e^-5	0.96	INTRON CG17839
2R	16158624	2R_16158624_SNP [dm3] 2R_20271119_SNP [dm6]	T	G	2.622e^-5	0.96	DOWNSTREAM CG10444 & 1 other INTERGENIC
3L	7631469	3L_7631469_SNP [dm3] 3L_7638369_SNP [dm6]	A	T	2.703e^-5	0.96	NON_SYNONYMOUS_CODING CG33275
2R	17982565	2R_17982565_SNP [dm3] 2R_22095060_SNP [dm6]	A	C	2.811e^-5	0.96	INTRON CG11073
2L	561970	2L_561970_SNP [dm3] 2L_561970_SNP [dm6]	T	C	2.820e^-5	0.96	SYNONYMOUS_CODING CG11835	TF binding site mE1_TFBS_chinmo
2L	2339075	2L_2339075_SNP [dm3] 2L_2339075_SNP [dm6]	T	C	2.823e^-5	0.96	SYNONYMOUS_CODING eys INTRON CG9967
2L	14315440	2L_14315440_SNP [dm3] 2L_14315440_SNP [dm6]	A	T	2.915e^-5	0.96	INTRON wb	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	3543206	3L_3543206_SNP [dm3] 3L_3543206_SNP [dm6]	T	A	3.020e^-5	0.96	UPSTREAM Eip63E INTRON Eip63E	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2L	14066824	2L_14066824_SNP [dm3] 2L_14066824_SNP [dm6]	T	A	3.135e^-5	0.96	INTRON nAChRalpha5
2R	20137954	2R_20137954_SNP [dm3] 2R_24250431_SNP [dm6]	C	T	3.223e^-5	0.96	SYNONYMOUS_CODING Ir60a UPSTREAM snoRNA:Me18S-A1597 INTRON nord	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	10883003	3L_10883003_SNP [dm3] 3L_10889903_SNP [dm6]	T	C	3.230e^-5	0.96	UPSTREAM Cpr67Fa1 INTERGENIC
2L	10548577	2L_10548577_SNP [dm3] 2L_10548577_SNP [dm6]	C	T	3.415e^-5	0.96	INTRON Trim9	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_cad mE1_TFBS_HSA
3L	3542717	3L_3542717_SNP [dm3] 3L_3542717_SNP [dm6]	C	T	3.496e^-5	0.96	UPSTREAM Eip63E INTRON Eip63E	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	12369802	3L_12369802_SNP [dm3] 3L_12376702_SNP [dm6]	C	A	3.580e^-5	0.96	INTRON Ncc69
2R	15385928	2R_15385928_SNP [dm3] 2R_19498423_SNP [dm6]	T	G	3.670e^-5	0.96	INTRON CG15120	TF binding site mE1_TFBS_cad
X	14858957	X_14858957_SNP [dm3] X_14964924_SNP [dm6]	G	A	3.709e^-5	0.96	INTRON eag
3L	9546282	3L_9546282_SNP [dm3] 3L_9553182_SNP [dm6]	A	T	3.794e^-5	0.96	UTR_5_PRIME CG42673
X	14860759	X_14860759_SNP [dm3] X_14966726_SNP [dm6]	C	A	3.953e^-5	0.96	INTRON eag
X	17014621	X_17014621_SNP [dm3] X_17120588_SNP [dm6]	G	A	3.956e^-5	0.96	INTRON CG5004
2L	7078028	2L_7078028_SNP [dm3] 2L_7078028_SNP [dm6]	T	C	4.134e^-5	0.96	DOWNSTREAM CR44611 INTRON Pvf2
3L	12897737	3L_12897737_SNP [dm3] 3L_12904637_SNP [dm6]	T	C	4.149e^-5	0.96	UPSTREAM CG32117 INTERGENIC
2L	10548524	2L_10548524_INS [dm3] 2L_10548524_INS [dm6]	A	AG	4.180e^-5	0.96	INTRON Trim9	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	9359040	3L_9359040_SNP [dm3] 3L_9365940_SNP [dm6]	A	G	4.198e^-5	0.96	SYNONYMOUS_CODING Klp67A DOWNSTREAM CG4447	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	14860763	X_14860763_SNP [dm3] X_14966730_SNP [dm6]	A	C	4.287e^-5	0.96	INTRON eag
X	5820058	X_5820058_SNP [dm3] X_5926025_SNP [dm6]	C	A	4.298e^-5	0.96	INTRON CG3726
3R	17527798	3R_17527798_SNP [dm3] 3R_21702076_SNP [dm6]	T	C	4.317e^-5	0.96	INTRON CG31176
X	10396239	X_10396239_SNP [dm3] X_10502206_SNP [dm6]	G	A	4.335e^-5	0.96	INTRON spri	TF binding site mE1_TFBS_inv
3R	13895629	3R_13895629_SNP [dm3] 3R_18069907_SNP [dm6]	C	T	4.377e^-5	0.96	INTERGENIC
2L	67830	2L_67830_SNP [dm3] 2L_67830_SNP [dm6]	T	G	4.389e^-5	0.96	INTRON dbr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_Trl
3L	3543152	3L_3543152_SNP [dm3] 3L_3543152_SNP [dm6]	G	A	4.392e^-5	0.96	UPSTREAM Eip63E INTRON Eip63E	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2R	16768035	2R_16768035_SNP [dm3] 2R_20880530_SNP [dm6]	G	A	4.481e^-5	0.96	INTRON Cib2
2L	2339048	2L_2339048_SNP [dm3] 2L_2339048_SNP [dm6]	A	G	4.489e^-5	0.96	SYNONYMOUS_CODING eys INTRON CG9967
3L	18319082	3L_18319082_SNP [dm3] 3L_18325982_SNP [dm6]	A	G	4.678e^-5	0.96	INTERGENIC
3L	5373501	3L_5373501_SNP [dm3] 3L_5380401_SNP [dm6]	G	T	4.678e^-5	0.96	SYNONYMOUS_CODING Ir64a
2L	9951369	2L_9951369_SNP [dm3] 2L_9951369_SNP [dm6]	C	G	4.745e^-5	0.96	UPSTREAM mir-87 DOWNSTREAM CG13126 INTERGENIC
X	10110203	X_10110203_SNP [dm3] X_10216170_SNP [dm6]	T	G	4.766e^-5	0.96	UTR_3_PRIME l_1_G0230 INTRON CG2962	TF binding site BDTNP1_TFBS_sna
3L	10636005	3L_10636005_SNP [dm3] 3L_10642905_SNP [dm6]	A	T	4.849e^-5	0.96	UTR_3_PRIME CG14154 UPSTREAM CG14153 INTRON CG32066
3R	14765182	3R_14765182_SNP [dm3] 3R_18939460_SNP [dm6]	A	G	4.915e^-5	0.96	INTRON CG42613
3L	9359713	3L_9359713_SNP [dm3] 3L_9366613_SNP [dm6]	G	A	5.090e^-5	0.96	SYNONYMOUS_CODING Klp67A UPSTREAM CG4452	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	12617248	2R_12617248_SNP [dm3] 2R_16729743_SNP [dm6]	A	C	5.106e^-5	0.96	INTRON CG30463
3R	7117238	3R_7117238_SNP [dm3] 3R_11291516_SNP [dm6]	T	A	5.185e^-5	0.96	INTRON CR31386
3R	4222188	3R_4222188_SNP [dm3] 3R_8396466_SNP [dm6]	T	C	5.313e^-5	0.96	INTRON CG45263
2L	13712206	2L_13712206_SNP [dm3] 2L_13712206_SNP [dm6]	T	C	5.315e^-5	0.96	INTRON CG31814
2L	9612734	2L_9612734_SNP [dm3] 2L_9612734_SNP [dm6]	G	C	5.322e^-5	0.96	UPSTREAM Trx-2 DOWNSTREAM gcm2 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_zfh1
3L	2633038	3L_2633038_SNP [dm3] 3L_2633038_SNP [dm6]	G	A	5.392e^-5	0.96	INTRON MEP-1 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	13059674	2R_13059674_SNP [dm3] 2R_17172169_SNP [dm6]	T	C	5.451e^-5	0.96	INTERGENIC
2R	18964316	2R_18964316_SNP [dm3] 2R_23076793_SNP [dm6]	T	G	5.562e^-5	0.96	NON_SYNONYMOUS_CODING Art7 UTR_3_PRIME CG3085	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	14829694	3L_14829694_SNP [dm3] 3L_14836594_SNP [dm6]	T	A	5.633e^-5	0.96	INTRON CG17839
3L	748416	3L_748416_SNP [dm3] 3L_748416_SNP [dm6]	T	C	5.692e^-5	0.96	UPSTREAM emc INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_ttk mE1_TFBS_Ubx
3R	19950779	3R_19950779_SNP [dm3] 3R_24125057_SNP [dm6]	C	T	5.722e^-5	0.96	SYNONYMOUS_CODING Rootletin	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	3899654	2L_3899654_SNP [dm3] 2L_3899654_SNP [dm6]	G	C	5.727e^-5	0.96	INTRON capu
2L	17344458	2L_17344458_SNP [dm3] 2L_17344458_SNP [dm6]	C	A	5.738e^-5	0.96	INTERGENIC
3L	19218496	3L_19218496_SNP [dm3] 3L_19225396_SNP [dm6]	T	G	5.761e^-5	0.96	INTRON fz2
2R	5395913	2R_5395913_SNP [dm3] 2R_9508408_SNP [dm6]	T	A	5.779e^-5	0.96	INTRON brp
3L	3543195	3L_3543195_SNP [dm3] 3L_3543195_SNP [dm6]	T	A	5.814e^-5	0.96	UPSTREAM Eip63E INTRON Eip63E	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
3L	18130346	3L_18130346_SNP [dm3] 3L_18137246_SNP [dm6]	T	A	5.862e^-5	0.96	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
X	17007539	X_17007539_SNP [dm3] X_17113506_SNP [dm6]	G	T	5.893e^-5	0.96	INTRON CG5004
3R	18449737	3R_18449737_SNP [dm3] 3R_22624015_SNP [dm6]	A	T	5.988e^-5	0.96	INTRON loco	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
2R	10948396	2R_10948396_SNP [dm3] 2R_15060891_SNP [dm6]	A	C	6.004e^-5	0.96	INTERGENIC

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

CG42404_CT phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results