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=7.696e^-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
wolba	0.09417
In_3R_K	0.06563
In_3R_Mo	0.03431

Kruskal-Wallis test

Covariate	χ²	p-value
wolba	3.7134	0.054
In_3R_P	6.6712	0.0356
In_3R_K	4.7628	0.0924
In_3R_Mo	4.6619	0.0972

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2348 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	6539726	3R_6539726_INS [dm3] 3R_10714004_INS [dm6]	T	TC	2.972e^-7	0.557	UPSTREAM CG4073 INTERGENIC
3L	8209863	3L_8209863_SNP [dm3] 3L_8216763_SNP [dm6]	A	G	9.810e^-7	0.646	DOWNSTREAM CG8012 INTERGENIC
3L	8209861	3L_8209861_INS [dm3] 3L_8216761_INS [dm6]	A	ATGTACATA	3.087e^-6	0.646	DOWNSTREAM CG8012 INTERGENIC
3L	10453062	3L_10453062_SNP [dm3] 3L_10459962_SNP [dm6]	A	T	3.289e^-6	0.646	NON_SYNONYMOUS_CODING Gem3	TF binding site mE1_TFBS_sens
3L	5542307	3L_5542307_SNP [dm3] 3L_5549207_SNP [dm6]	G	C	3.655e^-6	0.646	INTRON CG10625
X	16164469	X_16164469_SNP [dm3] X_16270436_SNP [dm6]	C	A	3.880e^-6	0.646	SYNONYMOUS_CODING kat80 UPSTREAM Mfe2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA
3R	16878253	3R_16878253_SNP [dm3] 3R_21052531_SNP [dm6]	A	T	5.207e^-6	0.646	DOWNSTREAM Mvl INTRON Mvl
3L	9961943	3L_9961943_SNP [dm3] 3L_9968843_SNP [dm6]	G	T	5.776e^-6	0.646	UTR_5_PRIME Nc UPSTREAM CG6685	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	23026861	3R_23026861_SNP [dm3] 3R_27201139_SNP [dm6]	G	A	6.369e^-6	0.646	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	12126989	2L_12126989_SNP [dm3] 2L_12126989_SNP [dm6]	C	T	6.623e^-6	0.646	NON_SYNONYMOUS_CODING CG17211
3R	19389699	3R_19389699_SNP [dm3] 3R_23563977_SNP [dm6]	T	A	6.848e^-6	0.646	INTRON beat-IV
2L	1471481	2L_1471481_SNP [dm3] 2L_1471481_SNP [dm6]	T	C	7.723e^-6	0.646	INTERGENIC	TF binding site mE1_TFBS_sens
2L	3979995	2L_3979995_SNP [dm3] 2L_3979995_SNP [dm6]	A	G	7.960e^-6	0.646	INTRON fred
3R	16321082	3R_16321082_SNP [dm3] 3R_20495360_SNP [dm6]	A	G	7.965e^-6	0.646	INTERGENIC
2L	3980075	2L_3980075_SNP [dm3] 2L_3980075_SNP [dm6]	G	T	8.773e^-6	0.646	INTRON fred
2L	20877925	2L_20877925_SNP [dm3] 2L_20877925_SNP [dm6]	T	G	8.891e^-6	0.646	INTRON sky & 1 other	TF binding site mE1_TFBS_cnc
X	20042639	X_20042639_DEL [dm3] X_20148606_DEL [dm6]	AA	A	9.404e^-6	0.646	INTRON CG9572
3R	16878254	3R_16878254_SNP [dm3] 3R_21052532_SNP [dm6]	T	A	9.416e^-6	0.646	DOWNSTREAM Mvl INTRON Mvl
2L	6106443	2L_6106443_SNP [dm3] 2L_6106443_SNP [dm6]	C	G	9.467e^-6	0.646	INTRON stai
3R	14361680	3R_14361680_SNP [dm3] 3R_18535958_SNP [dm6]	A	T	9.548e^-6	0.646	INTRON fru
3L	10080404	3L_10080404_SNP [dm3] 3L_10087304_SNP [dm6]	A	G	9.985e^-6	0.646	SYNONYMOUS_CODING CG14160 INTRON dpr6	TF binding site mE1_TFBS_cad
3L	16521827	3L_16521827_SNP [dm3] 3L_16528727_SNP [dm6]	T	C	1.008e^-5	0.646	INTRON CG43373
X	16164857	X_16164857_SNP [dm3] X_16270824_SNP [dm6]	G	A	1.027e^-5	0.646	UPSTREAM Mfe2 INTRON kat80	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_jumu
2L	82497	2L_82497_SNP [dm3] 2L_82497_SNP [dm6]	C	T	1.114e^-5	0.646	UTR_3_PRIME net DOWNSTREAM net
3L	11625548	3L_11625548_SNP [dm3] 3L_11632448_SNP [dm6]	G	T	1.218e^-5	0.646	DOWNSTREAM CR45158 INTRON CG32091
2R	15257523	2R_15257523_SNP [dm3] 2R_19370018_SNP [dm6]	G	A	1.351e^-5	0.646	SYNONYMOUS_CODING CG9416
3R	26129471	3R_26129471_SNP [dm3] 3R_30303749_SNP [dm6]	A	T	1.357e^-5	0.646	INTRON hdc
3L	10080401	3L_10080401_SNP [dm3] 3L_10087301_SNP [dm6]	C	T	1.414e^-5	0.646	SYNONYMOUS_CODING CG14160 INTRON dpr6	TF binding site mE1_TFBS_cad
2L	3979929	2L_3979929_SNP [dm3] 2L_3979929_SNP [dm6]	A	C	1.459e^-5	0.646	INTRON fred
3R	25667014	3R_25667014_SNP [dm3] 3R_29841292_SNP [dm6]	A	G	1.525e^-5	0.646	UPSTREAM Cad99C INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_inv
X	13127084	X_13127084_SNP [dm3] X_13233051_SNP [dm6]	C	T	1.538e^-5	0.646	INTRON mew	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	15257501	2R_15257501_SNP [dm3] 2R_19369996_SNP [dm6]	G	A	1.550e^-5	0.646	SYNONYMOUS_CODING CG9416
3L	10895491	3L_10895491_SNP [dm3] 3L_10902391_SNP [dm6]	C	T	1.588e^-5	0.646	INTERGENIC
3L	6472019	3L_6472019_SNP [dm3] 3L_6478919_SNP [dm6]	T	A	1.647e^-5	0.646	INTRON CG42747
2R	15257547	2R_15257547_SNP [dm3] 2R_19370042_SNP [dm6]	T	G	1.663e^-5	0.646	SYNONYMOUS_CODING CG9416
2R	15257583	2R_15257583_SNP [dm3] 2R_19370078_SNP [dm6]	T	C	1.677e^-5	0.646	SYNONYMOUS_CODING CG9416
2R	16931661	2R_16931661_SNP [dm3] 2R_21044156_SNP [dm6]	T	C	1.690e^-5	0.646	INTERGENIC	TF binding site mE1_TFBS_sens
3R	14618653	3R_14618653_SNP [dm3] 3R_18792931_SNP [dm6]	T	A	1.702e^-5	0.646	UPSTREAM CG7720 INTRON CG7720
X	16165143	X_16165143_SNP [dm3] X_16271110_SNP [dm6]	T	A	1.779e^-5	0.646	UPSTREAM Mfe2 INTRON kat80 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
3L	8212651	3L_8212651_SNP [dm3] 3L_8219551_SNP [dm6]	C	A	1.789e^-5	0.646	UPSTREAM CG13674 INTERGENIC
3R	22958993	3R_22958993_SNP [dm3] 3R_27133271_SNP [dm6]	A	T	1.884e^-5	0.646	INTRON CG6051
3L	296943	3L_296943_SNP [dm3] 3L_296943_SNP [dm6]	A	C	1.885e^-5	0.646	UPSTREAM RhoGEF3 INTRON RhoGEF3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	25887666	3R_25887666_SNP [dm3] 3R_30061944_SNP [dm6]	A	G	1.889e^-5	0.646	UPSTREAM sima INTRON sima	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	17227525	2R_17227525_SNP [dm3] 2R_21340020_SNP [dm6]	T	C	1.922e^-5	0.646	SYNONYMOUS_CODING dom	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	26943202	3R_26943202_SNP [dm3] 3R_31117480_SNP [dm6]	A	T	1.923e^-5	0.646	INTERGENIC
2L	2187811	2L_2187811_INS [dm3] 2L_2187811_INS [dm6]	G	GG	1.930e^-5	0.646	DOWNSTREAM tRNA:CR31946 & 1 other EXON CR44066	TF binding site mE1_TFBS_chinmo
3R	25886176	3R_25886176_SNP [dm3] 3R_30060454_SNP [dm6]	C	T	1.930e^-5	0.646	INTRON sima	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	8499049	2L_8499049_SNP [dm3] 2L_8499049_SNP [dm6]	G	C	1.954e^-5	0.646	INTRON Dh31
3R	16878239	3R_16878239_SNP [dm3] 3R_21052517_SNP [dm6]	A	G	1.995e^-5	0.646	DOWNSTREAM Mvl INTRON Mvl
3L	6472008	3L_6472008_SNP [dm3] 3L_6478908_SNP [dm6]	A	C	2.056e^-5	0.646	INTRON CG42747
2R	14785634	2R_14785634_SNP [dm3] 2R_18898129_SNP [dm6]	T	C	2.057e^-5	0.646	INTRON sano
3R	22959086	3R_22959086_SNP [dm3] 3R_27133364_SNP [dm6]	G	T	2.063e^-5	0.646	INTRON CG6051
3L	5347689	3L_5347689_SNP [dm3] 3L_5354589_SNP [dm6]	C	T	2.069e^-5	0.646	INTRON lama	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	20133685	3R_20133685_SNP [dm3] 3R_24307963_SNP [dm6]	C	A	2.073e^-5	0.646	INTRON crb
3L	18756200	3L_18756200_INS [dm3] 3L_18763100_INS [dm6]	GGC	ATTATA	2.091e^-5	0.646	INTRON ftz-f1
X	20042717	X_20042717_SNP [dm3] X_20148684_SNP [dm6]	T	C	2.168e^-5	0.646	INTRON CG9572
2L	3300912	2L_3300912_SNP [dm3] 2L_3300912_SNP [dm6]	T	G	2.209e^-5	0.646	INTRON CG9663
X	16165237	X_16165237_SNP [dm3] X_16271204_SNP [dm6]	A	C	2.223e^-5	0.646	UPSTREAM Mfe2 INTRON kat80 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
3R	16493056	3R_16493056_SNP [dm3] 3R_20667334_SNP [dm6]	T	A	2.279e^-5	0.646	INTERGENIC
2R	15257406	2R_15257406_INS [dm3] 2R_19369901_INS [dm6]	T	TA	2.321e^-5	0.646	INTRON CG9416
3L	5672282	3L_5672282_SNP [dm3] 3L_5679182_SNP [dm6]	A	C	2.331e^-5	0.646	UTR_5_PRIME sif INTRON sif
3L	6472014	3L_6472014_SNP [dm3] 3L_6478914_SNP [dm6]	G	A	2.340e^-5	0.646	INTRON CG42747
X	16165160	X_16165160_DEL [dm3] X_16271127_DEL [dm6]	TGT	T	2.400e^-5	0.646	UPSTREAM Mfe2 INTRON kat80 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
3R	16878201	3R_16878201_SNP [dm3] 3R_21052479_SNP [dm6]	A	T	2.482e^-5	0.646	DOWNSTREAM Mvl INTRON Mvl
3R	26916453	3R_26916453_SNP [dm3] 3R_31090731_SNP [dm6]	T	A	2.521e^-5	0.646	UTR_3_PRIME CG11317
3R	26916454	3R_26916454_SNP [dm3] 3R_31090732_SNP [dm6]	T	A	2.521e^-5	0.646	UTR_3_PRIME CG11317
3R	26916456	3R_26916456_DEL [dm3] 3R_31090734_DEL [dm6]	TTG	T	2.521e^-5	0.646	UTR_3_PRIME CG11317
3R	26916461	3R_26916461_SNP [dm3] 3R_31090739_SNP [dm6]	A	T	2.521e^-5	0.646	UTR_3_PRIME CG11317
3R	26916463	3R_26916463_SNP [dm3] 3R_31090741_SNP [dm6]	A	G	2.521e^-5	0.646	UTR_3_PRIME CG11317
3L	8209874	3L_8209874_SNP [dm3] 3L_8216774_SNP [dm6]	G	A	2.558e^-5	0.646	DOWNSTREAM CG8012 INTERGENIC
2R	15257418	2R_15257418_SNP [dm3] 2R_19369913_SNP [dm6]	A	G	2.615e^-5	0.646	INTRON CG9416
X	13127116	X_13127116_SNP [dm3] X_13233083_SNP [dm6]	A	G	2.631e^-5	0.646	INTRON mew	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	26020908	3R_26020908_SNP [dm3] 3R_30195186_SNP [dm6]	G	A	2.642e^-5	0.646	SYNONYMOUS_CODING CG15531
3L	10080332	3L_10080332_SNP [dm3] 3L_10087232_SNP [dm6]	A	G	2.671e^-5	0.646	SYNONYMOUS_CODING CG14160 INTRON dpr6
2L	6826581	2L_6826581_SNP [dm3] 2L_6826581_SNP [dm6]	C	T	2.703e^-5	0.646	INTRON sens-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
X	11847104	X_11847104_SNP [dm3] X_11953071_SNP [dm6]	T	C	2.767e^-5	0.646	INTRON cac	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	11778100	X_11778100_SNP [dm3] X_11884067_SNP [dm6]	T	C	2.768e^-5	0.646	INTRON CG10353
3R	26916466	3R_26916466_SNP [dm3] 3R_31090744_SNP [dm6]	C	A	2.778e^-5	0.646	UTR_3_PRIME CG11317
3L	6472044	3L_6472044_SNP [dm3] 3L_6478944_SNP [dm6]	G	T	2.829e^-5	0.646	INTRON CG42747
3L	5542352	3L_5542352_SNP [dm3] 3L_5549252_SNP [dm6]	A	G	2.844e^-5	0.646	INTRON CG10625
3R	7424627	3R_7424627_SNP [dm3] 3R_11598905_SNP [dm6]	T	C	2.874e^-5	0.646	INTRON Jupiter
2L	7246926	2L_7246926_SNP [dm3] 2L_7246926_SNP [dm6]	G	C	2.903e^-5	0.646	INTRON Ndae1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	6213965	2L_6213965_SNP [dm3] 2L_6213965_SNP [dm6]	T	C	2.906e^-5	0.646	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr
3L	5542342	3L_5542342_INS [dm3] 3L_5549242_INS [dm6]	G	GT	2.910e^-5	0.646	INTRON CG10625
2L	4296137	2L_4296137_SNP [dm3] 2L_4296137_SNP [dm6]	A	G	2.991e^-5	0.646	INTRON tutl
2L	18445089	2L_18445089_SNP [dm3] 2L_18445089_SNP [dm6]	G	A	3.007e^-5	0.646	SYNONYMOUS_CODING ncm	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	7900460	3L_7900460_SNP [dm3] 3L_7907360_SNP [dm6]	G	A	3.021e^-5	0.646	INTRON pbl
2L	109123	2L_109123_SNP [dm3] 2L_109123_SNP [dm6]	G	A	3.092e^-5	0.646	UPSTREAM Sam-S INTRON Sam-S	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	4591322	2L_4591322_SNP [dm3] 2L_4591322_SNP [dm6]	G	T	3.110e^-5	0.646	INTRON dp
X	20042708	X_20042708_SNP [dm3] X_20148675_SNP [dm6]	G	A	3.128e^-5	0.646	INTRON CG9572
3L	5357788	3L_5357788_SNP [dm3] 3L_5364688_SNP [dm6]	A	G	3.136e^-5	0.646	INTRON Uev1A	TF binding site mE1_TFBS_inv
2L	4320521	2L_4320521_SNP [dm3] 2L_4320521_SNP [dm6]	C	T	3.234e^-5	0.648	SYNONYMOUS_CODING tutl UTR_3_PRIME tutl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	6539705	3R_6539705_INS [dm3] 3R_10713983_INS [dm6]	C	CGC	3.257e^-5	0.648	UPSTREAM CG4073 INTERGENIC
X	10058673	X_10058673_SNP [dm3] X_10164640_SNP [dm6]	T	C	3.272e^-5	0.648	INTRON CR44894 & 1 other	TF binding site mE1_TFBS_chinmo
X	16163159	X_16163159_SNP [dm3] X_16269126_SNP [dm6]	T	G	3.305e^-5	0.648	SYNONYMOUS_CODING kat80
2R	10827445	2R_10827445_SNP [dm3] 2R_14939940_SNP [dm6]	G	A	3.315e^-5	0.648	UTR_3_PRIME Lap1
2L	14456068	2L_14456068_SNP [dm3] 2L_14456068_SNP [dm6]	T	G	3.370e^-5	0.652	INTERGENIC	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_sbb
2R	17265123	2R_17265123_SNP [dm3] 2R_21377618_SNP [dm6]	C	G	3.510e^-5	0.653	INTRON cv-2
2R	7465354	2R_7465354_SNP [dm3] 2R_11577849_SNP [dm6]	T	C	3.549e^-5	0.653	UTR_3_PRIME tou
X	16164738	X_16164738_SNP [dm3] X_16270705_SNP [dm6]	G	A	3.585e^-5	0.653	UPSTREAM Mfe2 INTRON kat80	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Mean phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results