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=3.575e^-18)
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_P	0.07204

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	5.1782	0.0751

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1714 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	15381018	2L_15381018_SNP [dm3] 2L_15381018_SNP [dm6]	C	G	4.591e^-7	0.861	INTERGENIC
2L	15381006	2L_15381006_SNP [dm3] 2L_15381006_SNP [dm6]	A	G	1.079e^-6	0.993	INTERGENIC
2L	8909454	2L_8909454_SNP [dm3] 2L_8909454_SNP [dm6]	A	C	2.360e^-6	0.993	INTRON CG34398
X	13881123	X_13881123_SNP [dm3] X_13987090_SNP [dm6]	C	T	3.477e^-6	0.993	UPSTREAM mamo INTRON mamo	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	19742844	3R_19742844_SNP [dm3] 3R_23917122_SNP [dm6]	T	C	3.875e^-6	0.993	INTRON sba	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3R	19742848	3R_19742848_SNP [dm3] 3R_23917126_SNP [dm6]	C	T	5.533e^-6	0.993	INTRON sba	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3L	3421941	3L_3421941_SNP [dm3] 3L_3421941_SNP [dm6]	T	G	5.561e^-6	0.993	INTRON sty
X	21527609	X_21527609_SNP [dm3] X_21656582_SNP [dm6]	T	C	5.674e^-6	0.993	INTERGENIC	transposable element FlyBase
2R	12866665	2R_12866665_SNP [dm3] 2R_16979160_SNP [dm6]	C	T	7.078e^-6	0.993	INTRON Cbp53E
2R	7259228	2R_7259228_SNP [dm3] 2R_11371723_SNP [dm6]	T	G	7.713e^-6	0.993	UPSTREAM Tapdelta INTERGENIC
X	21526601	X_21526601_SNP [dm3] X_21655574_SNP [dm6]	C	T	7.802e^-6	0.993	INTERGENIC	transposable element FlyBase
2L	1300626	2L_1300626_SNP [dm3] 2L_1300626_SNP [dm6]	T	A	8.576e^-6	0.993	INTERGENIC
X	18256461	X_18256461_SNP [dm3] X_18362428_SNP [dm6]	A	T	8.875e^-6	0.993	UTR_3_PRIME CG6106 DOWNSTREAM CG6106
3R	19742845	3R_19742845_SNP [dm3] 3R_23917123_SNP [dm6]	G	A	1.025e^-5	0.993	INTRON sba	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	14656756	2L_14656756_SNP [dm3] 2L_14656756_SNP [dm6]	C	G	1.056e^-5	0.993	INTRON osp
2L	12619482	2L_12619482_SNP [dm3] 2L_12619482_SNP [dm6]	C	T	1.108e^-5	0.993	INTRON Ref2 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	12814623	2R_12814623_INS [dm3] 2R_16927118_INS [dm6]	A	AAA	1.246e^-5	0.993	INTRON Pkc53E
3L	17256022	3L_17256022_SNP [dm3] 3L_17262922_SNP [dm6]	T	C	1.421e^-5	0.993	INTRON CR43870
3R	19742859	3R_19742859_DEL [dm3] 3R_23917137_DEL [dm6]	ATA	A	1.508e^-5	0.993	INTRON sba	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	12619458	2L_12619458_SNP [dm3] 2L_12619458_SNP [dm6]	C	T	1.550e^-5	0.993	INTRON Ref2 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	856437	3L_856437_SNP [dm3] 3L_856437_SNP [dm6]	T	G	1.747e^-5	0.993	NON_SYNONYMOUS_CODING dpr20
3L	3045822	3L_3045822_SNP [dm3] 3L_3045822_SNP [dm6]	C	T	1.803e^-5	0.993	NON_SYNONYMOUS_CODING scramb2	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_sens
3R	19742855	3R_19742855_SNP [dm3] 3R_23917133_SNP [dm6]	G	A	1.949e^-5	0.993	INTRON sba	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	14656807	2L_14656807_SNP [dm3] 2L_14656807_SNP [dm6]	A	C	2.019e^-5	0.993	INTRON osp
3L	8586477	3L_8586477_SNP [dm3] 3L_8593377_SNP [dm6]	A	G	2.052e^-5	0.993	INTRON CG43078
2R	19265034	2R_19265034_SNP [dm3] 2R_23377511_SNP [dm6]	A	G	2.073e^-5	0.993	UPSTREAM Golgin245 DOWNSTREAM CG13551 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2L	9370084	2L_9370084_INS [dm3] 2L_9370084_INS [dm6]	G	GGG	2.087e^-5	0.993	DOWNSTREAM Shawl INTERGENIC
2L	8363433	2L_8363433_DEL [dm3] 2L_8363433_DEL [dm6]	CC	C	2.400e^-5	0.993	UPSTREAM CG7627 DOWNSTREAM RpS13 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z
2L	12612676	2L_12612676_SNP [dm3] 2L_12612676_SNP [dm6]	A	G	2.434e^-5	0.993	INTRON nub & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
3L	1770622	3L_1770622_SNP [dm3] 3L_1770622_SNP [dm6]	T	G	2.455e^-5	0.993	SYNONYMOUS_CODING Dhc62B	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	16794374	2L_16794374_SNP [dm3] 2L_16794374_SNP [dm6]	A	G	2.600e^-5	0.993	NON_SYNONYMOUS_CODING Ugt36Ba DOWNSTREAM CG17928	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	3517574	3L_3517574_SNP [dm3] 3L_3517574_SNP [dm6]	C	A	2.618e^-5	0.993	INTRON Eip63E	TF binding site BDTNP1_TFBS_twi
3R	17657429	3R_17657429_SNP [dm3] 3R_21831707_SNP [dm6]	A	T	2.633e^-5	0.993	UPSTREAM Gr93a INTERGENIC
3R	4837211	3R_4837211_SNP [dm3] 3R_9011489_SNP [dm6]	C	A	2.668e^-5	0.993	NON_SYNONYMOUS_CODING CG11984	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	9759815	3R_9759815_SNP [dm3] 3R_13934093_SNP [dm6]	G	A	2.826e^-5	0.993	INTERGENIC
X	21526848	X_21526848_SNP [dm3] X_21655821_SNP [dm6]	T	A	2.873e^-5	0.993	INTERGENIC	transposable element FlyBase
X	21527157	X_21527157_SNP [dm3] X_21656130_SNP [dm6]	G	A	3.192e^-5	0.993	INTERGENIC
3L	9191555	3L_9191555_SNP [dm3] 3L_9198455_SNP [dm6]	T	G	3.217e^-5	0.993	INTERGENIC
2L	14656276	2L_14656276_SNP [dm3] 2L_14656276_SNP [dm6]	C	T	3.225e^-5	0.993	INTRON osp
2L	9369837	2L_9369837_SNP [dm3] 2L_9369837_SNP [dm6]	G	A	3.297e^-5	0.993	DOWNSTREAM Shawl INTERGENIC
2L	9370178	2L_9370178_SNP [dm3] 2L_9370178_SNP [dm6]	G	T	3.299e^-5	0.993	DOWNSTREAM Shawl INTERGENIC
3L	6998159	3L_6998159_SNP [dm3] 3L_7005059_SNP [dm6]	T	C	3.388e^-5	0.993	INTRON Mp
X	18255029	X_18255029_SNP [dm3] X_18360996_SNP [dm6]	T	C	3.436e^-5	0.993	INTRON CG6106
2L	12619410	2L_12619410_SNP [dm3] 2L_12619410_SNP [dm6]	A	T	3.515e^-5	0.993	INTRON Ref2 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	13597849	3R_13597849_SNP [dm3] 3R_17772127_SNP [dm6]	G	A	3.571e^-5	0.993	INTRON CG43102
3L	1769914	3L_1769914_SNP [dm3] 3L_1769914_SNP [dm6]	A	G	3.695e^-5	0.993	SYNONYMOUS_CODING Dhc62B	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	15365163	2L_15365163_SNP [dm3] 2L_15365163_SNP [dm6]	T	G	3.975e^-5	0.993	INTERGENIC
2L	15096922	2L_15096922_SNP [dm3] 2L_15096922_SNP [dm6]	A	G	4.178e^-5	0.993	DOWNSTREAM CG15270 INTERGENIC
3R	25103675	3R_25103675_SNP [dm3] 3R_29277953_SNP [dm6]	A	T	4.234e^-5	0.993	UPSTREAM CR45568 INTERGENIC	regulatory region REDfly_CRMs
3R	4446723	3R_4446723_SNP [dm3] 3R_8621001_SNP [dm6]	A	G	4.241e^-5	0.993	INTRON 5-HT2B	TF binding site mE1_TFBS_disco mE1_TFBS_HSA
2L	12610240	2L_12610240_SNP [dm3] 2L_12610240_SNP [dm6]	G	A	4.274e^-5	0.993	DOWNSTREAM Ref2 INTRON nub	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	14608968	3L_14608968_SNP [dm3] 3L_14615868_SNP [dm6]	T	A	4.292e^-5	0.993	INTRON shd
2L	16099725	2L_16099725_SNP [dm3] 2L_16099725_SNP [dm6]	C	A	4.374e^-5	0.993	INTERGENIC
2R	17883300	2R_17883300_SNP [dm3] 2R_21995795_SNP [dm6]	C	G	4.453e^-5	0.993	INTRON CG34370
2L	9494729	2L_9494729_SNP [dm3] 2L_9494729_SNP [dm6]	C	T	4.466e^-5	0.993	UTR_5_PRIME Gdi UPSTREAM CG33298	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl mE1_TFBS_Ubx
2L	7770874	2L_7770874_SNP [dm3] 2L_7770874_SNP [dm6]	C	A	4.505e^-5	0.993	INTRON CG7191
3L	11051684	3L_11051684_SNP [dm3] 3L_11058584_SNP [dm6]	T	C	4.541e^-5	0.993	SYNONYMOUS_CODING CG7888 DOWNSTREAM CG6321	TF binding site mE1_TFBS_cad
3L	8693954	3L_8693954_SNP [dm3] 3L_8700854_SNP [dm6]	T	A	4.630e^-5	0.993	INTERGENIC	silencer mE1_HDAC_PRE TF binding site mE1_TFBS_cad
2L	8324226	2L_8324226_SNP [dm3] 2L_8324226_SNP [dm6]	A	G	4.655e^-5	0.993	INTRON CG7781
3R	17657428	3R_17657428_SNP [dm3] 3R_21831706_SNP [dm6]	A	T	4.755e^-5	0.993	UPSTREAM Gr93a INTERGENIC
3R	8129436	3R_8129436_SNP [dm3] 3R_12303714_SNP [dm6]	A	G	4.759e^-5	0.993	DOWNSTREAM svp INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
2L	8325469	2L_8325469_SNP [dm3] 2L_8325469_SNP [dm6]	A	C	4.760e^-5	0.993	UPSTREAM CG7781 INTERGENIC
2L	8911138	2L_8911138_SNP [dm3] 2L_8911138_SNP [dm6]	T	C	5.145e^-5	0.993	INTRON CG34398
X	13000053	X_13000053_SNP [dm3] X_13106020_SNP [dm6]	A	T	5.154e^-5	0.993	INTRON CG43313
3R	24043651	3R_24043651_SNP [dm3] 3R_28217929_SNP [dm6]	C	A	5.218e^-5	0.993	INTRON CG34354
3R	14786726	3R_14786726_SNP [dm3] 3R_18961004_SNP [dm6]	A	G	5.223e^-5	0.993	INTRON CG42613 & 1 other
2L	5662309	2L_5662309_SNP [dm3] 2L_5662309_SNP [dm6]	G	C	5.251e^-5	0.993	UPSTREAM Hsp60C & 1 other INTERGENIC
X	5872349	X_5872349_SNP [dm3] X_5978316_SNP [dm6]	T	A	5.626e^-5	0.993	INTRON Grip
X	20117723	X_20117723_SNP [dm3] X_20246649_SNP [dm6]	A	T	5.639e^-5	0.993	INTRON Peritrophin-A	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	20117730	X_20117730_SNP [dm3] X_20246656_SNP [dm6]	A	G	5.639e^-5	0.993	INTRON Peritrophin-A	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	6427355	X_6427355_SNP [dm3] X_6533322_SNP [dm6]	G	A	5.670e^-5	0.993	UTR_5_PRIME RpL7A UPSTREAM RpL7A & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Ubx
2L	3402071	2L_3402071_SNP [dm3] 2L_3402071_SNP [dm6]	G	C	5.730e^-5	0.993	INTERGENIC
3R	22741117	3R_22741117_INS [dm3] 3R_26915395_INS [dm6]	T	TTAT	5.749e^-5	0.993	UPSTREAM sda INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18674071	2R_18674071_SNP [dm3] 2R_22786566_SNP [dm6]	A	G	5.787e^-5	0.993	INTRON CG42260
3R	24049661	3R_24049661_SNP [dm3] 3R_28223939_SNP [dm6]	A	G	5.797e^-5	0.993	INTRON CG34354
2L	9369813	2L_9369813_SNP [dm3] 2L_9369813_SNP [dm6]	A	G	5.993e^-5	0.993	DOWNSTREAM Shawl INTERGENIC
2R	12866549	2R_12866549_SNP [dm3] 2R_16979044_SNP [dm6]	T	G	6.082e^-5	0.993	INTRON Cbp53E
2L	8327092	2L_8327092_SNP [dm3] 2L_8327092_SNP [dm6]	C	T	6.083e^-5	0.993	UPSTREAM CG14275 INTERGENIC
X	9249253	X_9249253_SNP [dm3] X_9355220_SNP [dm6]	T	G	6.216e^-5	0.993	INTRON CG34449	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
2L	1284929	2L_1284929_SNP [dm3] 2L_1284929_SNP [dm6]	C	A	6.281e^-5	0.993	INTRON robo3
3R	15135409	3R_15135409_SNP [dm3] 3R_19309687_SNP [dm6]	G	A	6.344e^-5	0.993	INTRON Dl
2L	5910551	2L_5910551_SNP [dm3] 2L_5910551_SNP [dm6]	G	A	6.371e^-5	0.993	SYNONYMOUS_CODING bchs UPSTREAM CG14000	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	26686144	3R_26686144_SNP [dm3] 3R_30860422_SNP [dm6]	C	T	6.578e^-5	0.993	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	24598230	3R_24598230_SNP [dm3] 3R_28772508_SNP [dm6]	G	A	6.655e^-5	0.993	INTERGENIC
3L	12305285	3L_12305285_SNP [dm3] 3L_12312185_SNP [dm6]	T	C	6.815e^-5	0.993	DOWNSTREAM CG44355 INTERGENIC
2R	19171724	2R_19171724_SNP [dm3] 2R_23284201_SNP [dm6]	T	G	6.945e^-5	0.993	UPSTREAM CG13541 & 1 other INTERGENIC
X	21510820	X_21510820_SNP [dm3] X_21639793_SNP [dm6]	C	A	6.961e^-5	0.993	INTERGENIC	transposable element FlyBase
2L	3048435	2L_3048435_SNP [dm3] 2L_3048435_SNP [dm6]	C	A	7.177e^-5	0.993	SPLICE_SITE_REGION v_2_k05816 UPSTREAM snRNA:U5:23D INTRON v_2_k05816	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
X	17328661	X_17328661_SNP [dm3] X_17434628_SNP [dm6]	T	C	7.261e^-5	0.993	INTRON CG12994
2R	18408325	2R_18408325_SNP [dm3] 2R_22520820_SNP [dm6]	A	G	7.316e^-5	0.993	INTRON px	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	10189837	2L_10189837_SNP [dm3] 2L_10189837_SNP [dm6]	C	T	7.362e^-5	0.993	UTR_3_PRIME CG31874 INTRON Sur	TF binding site mE1_TFBS_cad
2L	10132956	2L_10132956_SNP [dm3] 2L_10132956_SNP [dm6]	C	G	7.406e^-5	0.993	INTRON CG44153
3R	22380910	3R_22380910_SNP [dm3] 3R_26555188_SNP [dm6]	A	T	7.425e^-5	0.993	INTRON scrib
2L	15096964	2L_15096964_SNP [dm3] 2L_15096964_SNP [dm6]	A	G	7.441e^-5	0.993	DOWNSTREAM CG15270 INTERGENIC
2R	11437694	2R_11437694_SNP [dm3] 2R_15550189_SNP [dm6]	A	G	7.523e^-5	0.993	UPSTREAM CG8192 INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_Trl
X	9248940	X_9248940_SNP [dm3] X_9354907_SNP [dm6]	A	T	7.614e^-5	0.993	UTR_5_PRIME CG34449	TF binding site BDTNP1_TFBS_dl
2L	15367292	2L_15367292_SNP [dm3] 2L_15367292_SNP [dm6]	A	T	7.622e^-5	0.993	INTERGENIC
2L	15381008	2L_15381008_SNP [dm3] 2L_15381008_SNP [dm6]	A	G	7.638e^-5	0.993	INTERGENIC
2R	12866554	2R_12866554_SNP [dm3] 2R_16979049_SNP [dm6]	A	G	7.707e^-5	0.993	INTRON Cbp53E
X	5293054	X_5293054_SNP [dm3] X_5399021_SNP [dm6]	C	T	7.716e^-5	0.993	INTRON SK

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By genomic position
Variant impact
Gene name

Nuclear_Consensu_Len phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results