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=1.697e^-3)
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_2L_t	0.007331
In_3R_Mo	0.043376

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	10.6046	0.005

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2016 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
2R	11575928	2R_11575928_SNP [dm3] 2R_15688423_SNP [dm6]	T	C	3.502e^-6	0.919	SYNONYMOUS_CODING Cep89	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	413912	3L_413912_SNP [dm3] 3L_413912_SNP [dm6]	C	T	3.723e^-6	0.919	INTERGENIC	TF binding site mE1_TFBS_Kr
3L	14555445	3L_14555445_SNP [dm3] 3L_14562345_SNP [dm6]	A	T	5.025e^-6	0.919	INTRON CG34039	TF binding site mE1_TFBS_bab1 mE1_TFBS_ttk
3L	16896011	3L_16896011_SNP [dm3] 3L_16902911_SNP [dm6]	A	T	5.898e^-6	0.919	NON_SYNONYMOUS_CODING Lmpt INTRON Lmpt	TF binding site mE1_TFBS_chinmo
2R	13506075	2R_13506075_SNP [dm3] 2R_17618570_SNP [dm6]	T	G	6.813e^-6	0.919	UPSTREAM CG44403 INTRON CG10936
2R	12116819	2R_12116819_SNP [dm3] 2R_16229314_SNP [dm6]	A	G	8.254e^-6	0.919	SYNONYMOUS_CODING Tsf3 UPSTREAM CG15701 INTRON CG15706	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	19127148	2R_19127148_SNP [dm3] 2R_23239625_SNP [dm6]	T	G	9.161e^-6	0.919	INTERGENIC
3L	14929590	3L_14929590_SNP [dm3] 3L_14936490_SNP [dm6]	G	C	9.359e^-6	0.919	INTRON DCX-EMAP
3L	743993	3L_743993_SNP [dm3] 3L_743993_SNP [dm6]	T	C	1.054e^-5	0.919	UPSTREAM tRNA:M-i:61D INTRON hng3	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10364938	3R_10364938_SNP [dm3] 3R_14539216_SNP [dm6]	G	T	1.090e^-5	0.919	INTRON Pde6
3L	15483312	3L_15483312_SNP [dm3] 3L_15490212_SNP [dm6]	A	G	1.592e^-5	0.919	INTERGENIC
3L	13553816	3L_13553816_DEL [dm3] 3L_13560716_DEL [dm6]	GTCGACGTAGCGACACT...	G	1.881e^-5	0.919	INTRON bru-3
2L	4144537	2L_4144537_SNP [dm3] 2L_4144537_SNP [dm6]	T	G	1.889e^-5	0.919	INTERGENIC
2L	18871861	2L_18871861_SNP [dm3] 2L_18871861_SNP [dm6]	G	A	1.902e^-5	0.919	INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	19522029	2L_19522029_SNP [dm3] 2L_19522029_SNP [dm6]	C	T	1.905e^-5	0.919	SYNONYMOUS_CODING CG10132	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	6463898	2L_6463898_SNP [dm3] 2L_6463898_SNP [dm6]	A	T	1.927e^-5	0.919	UTR_5_PRIME CG16947	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2L	18871864	2L_18871864_SNP [dm3] 2L_18871864_SNP [dm6]	C	T	1.946e^-5	0.919	INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	20316757	2R_20316757_SNP [dm3] 2R_24429234_SNP [dm6]	A	G	2.030e^-5	0.919	UPSTREAM prom DOWNSTREAM CG15873 INTERGENIC
X	20262267	X_20262267_SNP [dm3] X_20391240_SNP [dm6]	A	G	2.033e^-5	0.919	UPSTREAM l_1_G0004 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7721690	3L_7721690_SNP [dm3] 3L_7728590_SNP [dm6]	T	G	2.105e^-5	0.919	NON_SYNONYMOUS_CODING CG8492 INTRON CG32373	TF binding site mE1_TFBS_sens
2R	17894354	2R_17894354_SNP [dm3] 2R_22006849_SNP [dm6]	A	G	2.157e^-5	0.919	INTRON CG34370
3L	15483333	3L_15483333_SNP [dm3] 3L_15490233_SNP [dm6]	T	C	2.159e^-5	0.919	INTERGENIC
3L	8391972	3L_8391972_SNP [dm3] 3L_8398872_SNP [dm6]	A	T	2.198e^-5	0.919	INTRON CG7120
2L	22020494	2L_22020494_SNP [dm3] 2L_22020494_SNP [dm6]	A	G	2.248e^-5	0.919	DOWNSTREAM CR33987 INTRON tio	TF binding site mE1_TFBS_Trl
2L	18871879	2L_18871879_SNP [dm3] 2L_18871879_SNP [dm6]	C	T	2.281e^-5	0.919	INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	10842862	3L_10842862_SNP [dm3] 3L_10849762_SNP [dm6]	T	C	2.312e^-5	0.919	DOWNSTREAM CR45169 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3R	7331866	3R_7331866_SNP [dm3] 3R_11506144_SNP [dm6]	C	T	2.440e^-5	0.919	DOWNSTREAM dpr5 INTERGENIC
2L	8986559	2L_8986559_SNP [dm3] 2L_8986559_SNP [dm6]	T	C	2.536e^-5	0.919	INTRON rost
2L	8986560	2L_8986560_SNP [dm3] 2L_8986560_SNP [dm6]	C	A	2.536e^-5	0.919	INTRON rost
3L	8391974	3L_8391974_SNP [dm3] 3L_8398874_SNP [dm6]	G	A	2.575e^-5	0.919	INTRON CG7120
3L	3143873	3L_3143873_SNP [dm3] 3L_3143873_SNP [dm6]	T	A	2.594e^-5	0.919	UTR_5_PRIME CG1291 UPSTREAM CG11537	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
X	20262270	X_20262270_INS [dm3] X_20391243_INS [dm6]	A	ATCAATAATAATTCAA...	2.759e^-5	0.919	UPSTREAM l_1_G0004 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11573868	2R_11573868_SNP [dm3] 2R_15686363_SNP [dm6]	C	T	2.823e^-5	0.919	SYNONYMOUS_CODING Ranbp11 UPSTREAM CG30082	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_chinmo
3L	7721688	3L_7721688_SNP [dm3] 3L_7728588_SNP [dm6]	A	G	2.834e^-5	0.919	NON_SYNONYMOUS_CODING CG8492 INTRON CG32373	TF binding site mE1_TFBS_sens
2L	10085825	2L_10085825_SNP [dm3] 2L_10085825_SNP [dm6]	C	T	2.928e^-5	0.919	INTRON CG44153
3L	7777439	3L_7777439_SNP [dm3] 3L_7784339_SNP [dm6]	C	T	2.935e^-5	0.919	INTRON CG32369
2R	16425872	2R_16425872_SNP [dm3] 2R_20538367_SNP [dm6]	T	C	3.021e^-5	0.919	DOWNSTREAM CG13427 & 1 other 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_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA transposable element FlyBase
3R	5121979	3R_5121979_SNP [dm3] 3R_9296257_SNP [dm6]	T	G	3.110e^-5	0.919	INTRON CG8861
3L	20821277	3L_20821277_SNP [dm3] 3L_20828177_SNP [dm6]	C	T	3.170e^-5	0.919	UTR_5_PRIME Pka-R1 UPSTREAM Pka-R1 INTRON Pka-R1
3L	16896018	3L_16896018_SNP [dm3] 3L_16902918_SNP [dm6]	G	A	3.291e^-5	0.919	NON_SYNONYMOUS_CODING Lmpt INTRON Lmpt	TF binding site mE1_TFBS_chinmo
2L	22297776	2L_22297776_SNP [dm3] 2L_22297776_SNP [dm6]	G	A	3.359e^-5	0.919	INTERGENIC	transposable element FlyBase
3L	10756244	3L_10756244_SNP [dm3] 3L_10763144_SNP [dm6]	A	G	3.506e^-5	0.919	INTERGENIC
3L	5886015	3L_5886015_SNP [dm3] 3L_5892915_SNP [dm6]	C	G	3.631e^-5	0.919	INTERGENIC
2L	3126389	2L_3126389_SNP [dm3] 2L_3126389_SNP [dm6]	C	T	3.732e^-5	0.919	NON_SYNONYMOUS_CODING toc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	510296	2L_510296_SNP [dm3] 2L_510296_SNP [dm6]	C	G	3.834e^-5	0.919	INTRON ush	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_Trl
3L	15411404	3L_15411404_SNP [dm3] 3L_15418304_SNP [dm6]	G	T	3.894e^-5	0.919	INTERGENIC
2R	10925619	2R_10925619_SNP [dm3] 2R_15038114_SNP [dm6]	A	G	4.076e^-5	0.919	INTRON hbs
3L	4152861	3L_4152861_SNP [dm3] 3L_4152861_SNP [dm6]	G	A	4.162e^-5	0.919	DOWNSTREAM CG1299 & 1 other INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13156683	2R_13156683_SNP [dm3] 2R_17269178_SNP [dm6]	T	C	4.234e^-5	0.919	INTRON mbl	TF binding site mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_run
2R	8137681	2R_8137681_SNP [dm3] 2R_12250176_SNP [dm6]	A	C	4.235e^-5	0.919	INTERGENIC
2L	21802262	2L_21802262_SNP [dm3] 2L_21802262_SNP [dm6]	A	G	4.248e^-5	0.919	INTERGENIC
2L	7337340	2L_7337340_SNP [dm3] 2L_7337340_SNP [dm6]	G	T	4.462e^-5	0.919	INTRON Wnt6
X	21081580	X_21081580_SNP [dm3] X_21210553_SNP [dm6]	A	G	4.463e^-5	0.919	INTRON CG32521
2L	13696626	2L_13696626_SNP [dm3] 2L_13696626_SNP [dm6]	G	A	4.519e^-5	0.919	INTRON CG31814
3L	712423	3L_712423_SNP [dm3] 3L_712423_SNP [dm6]	G	C	4.568e^-5	0.919	UPSTREAM CG13896 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_zfh1
X	12850971	X_12850971_SNP [dm3] X_12956938_SNP [dm6]	G	T	4.642e^-5	0.919	INTRON hec
3R	21876370	3R_21876370_SNP [dm3] 3R_26050648_SNP [dm6]	T	G	4.669e^-5	0.919	SYNONYMOUS_CODING Exo84 DOWNSTREAM gro	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	20231634	3R_20231634_SNP [dm3] 3R_24405912_SNP [dm6]	G	A	4.714e^-5	0.919	INTRON nAChRalpha1
3L	742989	3L_742989_SNP [dm3] 3L_742989_SNP [dm6]	C	A	4.795e^-5	0.919	DOWNSTREAM tRNA:M-i:61D INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2L	18872053	2L_18872053_SNP [dm3] 2L_18872053_SNP [dm6]	C	A	4.864e^-5	0.919	INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	20946369	2R_20946369_SNP [dm3] 2R_25058846_SNP [dm6]	C	T	4.868e^-5	0.919	INTERGENIC	regulatory region FlyBase REDfly_CRMs
3L	3090995	3L_3090995_SNP [dm3] 3L_3090995_SNP [dm6]	C	T	4.873e^-5	0.919	UTR_3_PRIME Cht7 DOWNSTREAM CG11486 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
2R	13415564	2R_13415564_SNP [dm3] 2R_17528059_SNP [dm6]	G	A	4.932e^-5	0.919	SYNONYMOUS_CODING Patronin
2R	8137710	2R_8137710_SNP [dm3] 2R_12250205_SNP [dm6]	C	A	4.970e^-5	0.919	INTERGENIC
3L	1903336	3L_1903336_SNP [dm3] 3L_1903336_SNP [dm6]	G	A	5.016e^-5	0.919	INTRON CG1887
2R	16868926	2R_16868926_SNP [dm3] 2R_20981421_SNP [dm6]	T	C	5.130e^-5	0.919	SYNONYMOUS_CODING CG9313	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	11724772	2R_11724772_SNP [dm3] 2R_15837267_SNP [dm6]	C	T	5.200e^-5	0.919	INTRON tun	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
2L	3439088	2L_3439088_SNP [dm3] 2L_3439088_SNP [dm6]	T	G	5.209e^-5	0.919	INTERGENIC
3L	457095	3L_457095_MNP [dm3] 3L_457095_MNP [dm6]	AATC	CTAT	5.235e^-5	0.919	INTRON klar	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	13925733	2L_13925733_SNP [dm3] 2L_13925733_SNP [dm6]	C	A	5.303e^-5	0.919	INTRON Ance-3
3R	20489476	3R_20489476_SNP [dm3] 3R_24663754_SNP [dm6]	G	T	5.433e^-5	0.919	INTRON slo	regulatory region REDfly_CRMs
3L	457066	3L_457066_DEL [dm3] 3L_457066_DEL [dm6]	AAACGTTCGACA...	A	5.495e^-5	0.919	INTRON klar	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	457083	3L_457083_DEL [dm3] 3L_457083_DEL [dm6]	CCCTAGATT	C	5.495e^-5	0.919	INTRON klar	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	461575	3L_461575_SNP [dm3] 3L_461575_SNP [dm6]	A	T	5.495e^-5	0.919	INTRON klar
3L	461577	3L_461577_SNP [dm3] 3L_461577_SNP [dm6]	T	A	5.495e^-5	0.919	INTRON klar
3L	461600	3L_461600_SNP [dm3] 3L_461600_SNP [dm6]	C	A	5.495e^-5	0.919	INTRON klar
3L	20187404	3L_20187404_SNP [dm3] 3L_20194304_SNP [dm6]	A	G	5.585e^-5	0.919	INTRON CG42674
2L	4143125	2L_4143125_DEL [dm3] 2L_4143125_DEL [dm6]	TAGATTGAATGTGAA...	T	5.688e^-5	0.919	INTERGENIC
3L	413923	3L_413923_SNP [dm3] 3L_413923_SNP [dm6]	A	G	5.708e^-5	0.919	INTERGENIC	TF binding site mE1_TFBS_Kr
X	14842540	X_14842540_SNP [dm3] X_14948507_SNP [dm6]	T	C	5.739e^-5	0.919	INTRON pdgy	TF binding site mE1_TFBS_HSA
2L	21802210	2L_21802210_SNP [dm3] 2L_21802210_SNP [dm6]	G	A	5.799e^-5	0.919	INTERGENIC
2R	10837352	2R_10837352_SNP [dm3] 2R_14949847_SNP [dm6]	A	G	5.816e^-5	0.919	UPSTREAM aPKC INTRON aPKC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	10691472	3L_10691472_SNP [dm3] 3L_10698372_SNP [dm6]	T	A	6.047e^-5	0.919	INTERGENIC
2R	11576547	2R_11576547_SNP [dm3] 2R_15689042_SNP [dm6]	A	G	6.048e^-5	0.919	UPSTREAM CG30090 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3L	14813948	3L_14813948_SNP [dm3] 3L_14820848_SNP [dm6]	G	A	6.117e^-5	0.919	INTRON CG17839
3L	14561076	3L_14561076_SNP [dm3] 3L_14567976_SNP [dm6]	T	C	6.145e^-5	0.919	SYNONYMOUS_CODING CG42758
2L	376777	2L_376777_SNP [dm3] 2L_376777_SNP [dm6]	G	A	6.152e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
3L	14389469	3L_14389469_SNP [dm3] 3L_14396369_SNP [dm6]	C	G	6.224e^-5	0.919	INTERGENIC
3R	3469607	3R_3469607_SNP [dm3] 3R_7643885_SNP [dm6]	C	T	6.234e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	7045208	2R_7045208_SNP [dm3] 2R_11157703_SNP [dm6]	C	A	6.251e^-5	0.919	INTRON CG13229
2L	4424389	2L_4424389_SNP [dm3] 2L_4424389_SNP [dm6]	G	A	6.285e^-5	0.919	INTRON CG15431
3L	15411491	3L_15411491_SNP [dm3] 3L_15418391_SNP [dm6]	C	G	6.328e^-5	0.919	INTERGENIC
3R	10365362	3R_10365362_SNP [dm3] 3R_14539640_SNP [dm6]	G	A	6.351e^-5	0.919	INTRON Pde6
3L	1561196	3L_1561196_SNP [dm3] 3L_1561196_SNP [dm6]	G	T	6.366e^-5	0.919	NON_SYNONYMOUS_CODING CG7879	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	20187373	3L_20187373_SNP [dm3] 3L_20194273_SNP [dm6]	G	T	6.374e^-5	0.919	INTRON CG42674
2L	18328109	2L_18328109_SNP [dm3] 2L_18328109_SNP [dm6]	C	G	6.454e^-5	0.919	INTRON Fas3
2R	8862122	2R_8862122_SNP [dm3] 2R_12974617_SNP [dm6]	G	A	6.504e^-5	0.919	INTRON Psc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4952040	2L_4952040_SNP [dm3] 2L_4952040_SNP [dm6]	T	C	6.508e^-5	0.919	DOWNSTREAM Jon25Bii INTERGENIC
2L	16759323	2L_16759323_SNP [dm3] 2L_16759323_SNP [dm6]	C	T	6.567e^-5	0.919	INTRON ppk17
3L	7719844	3L_7719844_SNP [dm3] 3L_7726744_SNP [dm6]	A	T	6.622e^-5	0.919	UPSTREAM CG7457 INTRON CG32373	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA

Showing 1 to 100 of 1,000 entries

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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=2.572e^-5)
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_2L_t	0.04214

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	7.3935	0.0248

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1839 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	743993	3L_743993_SNP [dm3] 3L_743993_SNP [dm6]	T	C	1.773e^-6	0.978	UPSTREAM tRNA:M-i:61D INTRON hng3	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16861770	2R_16861770_SNP [dm3] 2R_20974265_SNP [dm6]	T	A	3.863e^-6	0.978	UPSTREAM CG15649 INTERGENIC
3L	7777439	3L_7777439_SNP [dm3] 3L_7784339_SNP [dm6]	C	T	5.617e^-6	0.978	INTRON CG32369
2R	6606992	2R_6606992_SNP [dm3] 2R_10719487_SNP [dm6]	A	T	8.431e^-6	0.978	INTRON stan
3L	12147115	3L_12147115_SNP [dm3] 3L_12154015_SNP [dm6]	T	C	9.465e^-6	0.978	SYNONYMOUS_CODING Nrx-IV
X	6477081	X_6477081_SNP [dm3] X_6583048_SNP [dm6]	G	T	9.510e^-6	0.978	SYNONYMOUS_CODING CG34417 INTRON CG34417
3R	6253276	3R_6253276_SNP [dm3] 3R_10427554_SNP [dm6]	G	A	9.695e^-6	0.978	INTERGENIC
3L	5886015	3L_5886015_SNP [dm3] 3L_5892915_SNP [dm6]	C	G	1.006e^-5	0.978	INTERGENIC
2L	11419352	2L_11419352_SNP [dm3] 2L_11419352_SNP [dm6]	A	G	1.059e^-5	0.978	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	10756244	3L_10756244_SNP [dm3] 3L_10763144_SNP [dm6]	A	G	1.102e^-5	0.978	INTERGENIC
2L	4364449	2L_4364449_SNP [dm3] 2L_4364449_SNP [dm6]	T	A	1.182e^-5	0.978	UPSTREAM CR45363 INTRON Traf4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	5544938	2L_5544938_SNP [dm3] 2L_5544938_SNP [dm6]	A	T	1.198e^-5	0.978	SYNONYMOUS_CODING Lam	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	9131327	2R_9131327_SNP [dm3] 2R_13243822_SNP [dm6]	G	A	1.238e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
3L	8391972	3L_8391972_SNP [dm3] 3L_8398872_SNP [dm6]	A	T	1.279e^-5	0.978	INTRON CG7120
2R	11251263	2R_11251263_SNP [dm3] 2R_15363758_SNP [dm6]	T	A	1.310e^-5	0.978	INTRON unc-5
3R	8486852	3R_8486852_SNP [dm3] 3R_12661130_SNP [dm6]	C	T	1.336e^-5	0.978	DOWNSTREAM CR45586 & 1 other INTERGENIC
3L	16983394	3L_16983394_SNP [dm3] 3L_16990294_SNP [dm6]	C	A	1.387e^-5	0.978	INTRON Exn
3R	19769710	3R_19769710_SNP [dm3] 3R_23943988_SNP [dm6]	G	A	1.424e^-5	0.978	SYNONYMOUS_CODING CG12268 UPSTREAM Gdh	TF binding site mE1_TFBS_cad
3L	8391974	3L_8391974_SNP [dm3] 3L_8398874_SNP [dm6]	G	A	1.451e^-5	0.978	INTRON CG7120
3L	16983298	3L_16983298_INS [dm3] 3L_16990198_INS [dm6]	A	AG	1.507e^-5	0.978	INTRON Exn
2R	9131300	2R_9131300_SNP [dm3] 2R_13243795_SNP [dm6]	A	T	1.547e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
3R	20509028	3R_20509028_SNP [dm3] 3R_24683306_SNP [dm6]	T	A	1.582e^-5	0.978	INTRON slo
3R	25760016	3R_25760016_SNP [dm3] 3R_29934294_SNP [dm6]	A	C	1.776e^-5	0.978	NON_SYNONYMOUS_CODING CG42558 UTR_3_PRIME CG42557 DOWNSTREAM eIF2B-alpha	TF binding site mE1_TFBS_cad
X	4865876	X_4865876_DEL [dm3] X_4971843_DEL [dm6]	ATATATATATATATAT...	A	1.827e^-5	0.978	INTRON CR44833	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	3090995	3L_3090995_SNP [dm3] 3L_3090995_SNP [dm6]	C	T	1.827e^-5	0.978	UTR_3_PRIME Cht7 DOWNSTREAM CG11486 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
3R	25759599	3R_25759599_SNP [dm3] 3R_29933877_SNP [dm6]	C	T	1.948e^-5	0.978	NON_SYNONYMOUS_CODING CG42557 START_GAINED CG42558 UTR_5_PRIME CG42558 UPSTREAM Cog7 DOWNSTREAM eIF2B-alpha	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	742989	3L_742989_SNP [dm3] 3L_742989_SNP [dm6]	C	A	1.984e^-5	0.978	DOWNSTREAM tRNA:M-i:61D INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
2R	9131489	2R_9131489_SNP [dm3] 2R_13243984_SNP [dm6]	G	T	2.050e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
2R	9131294	2R_9131294_SNP [dm3] 2R_13243789_SNP [dm6]	A	C	2.105e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
3R	6253307	3R_6253307_SNP [dm3] 3R_10427585_SNP [dm6]	G	T	2.423e^-5	0.978	INTERGENIC
3L	4152861	3L_4152861_SNP [dm3] 3L_4152861_SNP [dm6]	G	A	2.701e^-5	0.978	DOWNSTREAM CG1299 & 1 other INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	20860404	2L_20860404_SNP [dm3] 2L_20860404_SNP [dm6]	C	T	2.725e^-5	0.978	INTRON CG9336
X	5826894	X_5826894_INS [dm3] X_5932861_INS [dm6]	T	TT	2.787e^-5	0.978	INTRON CG3726
X	10443026	X_10443026_SNP [dm3] X_10548993_SNP [dm6]	C	T	2.836e^-5	0.978	INTRON spri
X	14756956	X_14756956_SNP [dm3] X_14862923_SNP [dm6]	A	C	2.852e^-5	0.978	DOWNSTREAM CG9518 INTRON Flo2
2R	9134428	2R_9134428_SNP [dm3] 2R_13246923_SNP [dm6]	A	G	2.856e^-5	0.978	NON_SYNONYMOUS_CODING Mp20	TF binding site mE1_TFBS_cad
2L	3439088	2L_3439088_SNP [dm3] 2L_3439088_SNP [dm6]	T	G	2.925e^-5	0.978	INTERGENIC
2L	4364464	2L_4364464_SNP [dm3] 2L_4364464_SNP [dm6]	C	G	3.022e^-5	0.978	UPSTREAM CR45363 INTRON Traf4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	18871879	2L_18871879_SNP [dm3] 2L_18871879_SNP [dm6]	C	T	3.083e^-5	0.978	INTRON tup	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	16331071	3L_16331071_SNP [dm3] 3L_16337971_SNP [dm6]	C	A	3.159e^-5	0.978	INTERGENIC
3L	743080	3L_743080_SNP [dm3] 3L_743080_SNP [dm6]	T	A	3.199e^-5	0.978	DOWNSTREAM tRNA:M-i:61D INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3L	1903336	3L_1903336_SNP [dm3] 3L_1903336_SNP [dm6]	G	A	3.204e^-5	0.978	INTRON CG1887
2R	9131495	2R_9131495_SNP [dm3] 2R_13243990_SNP [dm6]	G	T	3.214e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
2R	20946369	2R_20946369_SNP [dm3] 2R_25058846_SNP [dm6]	C	T	3.237e^-5	0.978	INTERGENIC	regulatory region FlyBase REDfly_CRMs
2R	9131331	2R_9131331_SNP [dm3] 2R_13243826_SNP [dm6]	A	C	3.296e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
2R	7045208	2R_7045208_SNP [dm3] 2R_11157703_SNP [dm6]	C	A	3.308e^-5	0.978	INTRON CG13229
3L	14057292	3L_14057292_SNP [dm3] 3L_14064192_SNP [dm6]	C	T	3.446e^-5	0.978	INTRON CG32138	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	12850971	X_12850971_SNP [dm3] X_12956938_SNP [dm6]	G	T	3.510e^-5	0.978	INTRON hec
X	2926031	X_2926031_SNP [dm3] X_3031998_SNP [dm6]	C	A	3.535e^-5	0.978	INTRON kirre
X	14756999	X_14756999_SNP [dm3] X_14862966_SNP [dm6]	A	G	3.677e^-5	0.978	DOWNSTREAM CG9518 INTRON Flo2
2R	20316757	2R_20316757_SNP [dm3] 2R_24429234_SNP [dm6]	A	G	3.915e^-5	0.978	UPSTREAM prom DOWNSTREAM CG15873 INTERGENIC
3L	743033	3L_743033_SNP [dm3] 3L_743033_SNP [dm6]	C	T	3.998e^-5	0.978	DOWNSTREAM tRNA:M-i:61D INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
X	21160844	X_21160844_SNP [dm3] X_21289817_SNP [dm6]	G	C	4.011e^-5	0.978	INTRON CG1494	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	14932148	2R_14932148_DEL [dm3] 2R_19044643_DEL [dm6]	AA	A	4.012e^-5	0.978	INTERGENIC
3L	1352726	3L_1352726_SNP [dm3] 3L_1352726_SNP [dm6]	A	G	4.089e^-5	0.978	UTR_3_PRIME 312 DOWNSTREAM 312 INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_zfh1
3L	2643105	3L_2643105_DEL [dm3] 3L_2643105_DEL [dm6]	TAATAT	T	4.116e^-5	0.978	INTRON CG14949
X	14842540	X_14842540_SNP [dm3] X_14948507_SNP [dm6]	T	C	4.173e^-5	0.978	INTRON pdgy	TF binding site mE1_TFBS_HSA
X	19401744	X_19401744_SNP [dm3] X_19507711_SNP [dm6]	T	C	4.202e^-5	0.978	SYNONYMOUS_CODING Pfrx INTRON CG14200	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14978893	2R_14978893_SNP [dm3] 2R_19091388_SNP [dm6]	C	T	4.325e^-5	0.978	SYNONYMOUS_CODING 5-HT1A
3L	7291341	3L_7291341_DEL [dm3] 3L_7298241_DEL [dm6]	GG	G	4.351e^-5	0.978	INTRON unc-13-4A
3L	12146645	3L_12146645_SNP [dm3] 3L_12153545_SNP [dm6]	T	C	4.363e^-5	0.978	SYNONYMOUS_CODING Nrx-IV
2L	4424389	2L_4424389_SNP [dm3] 2L_4424389_SNP [dm6]	G	A	4.401e^-5	0.978	INTRON CG15431
2R	9131453	2R_9131453_SNP [dm3] 2R_13243948_SNP [dm6]	A	C	4.500e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
2L	11930045	2L_11930045_SNP [dm3] 2L_11930045_SNP [dm6]	C	T	4.625e^-5	0.978	INTERGENIC
3L	8362346	3L_8362346_SNP [dm3] 3L_8369246_SNP [dm6]	C	T	4.635e^-5	0.978	INTERGENIC	TF binding site mE1_TFBS_bab1
3L	742992	3L_742992_DEL [dm3] 3L_742992_DEL [dm6]	ATGGTTTTTGATAACTAA...	A	4.683e^-5	0.978	DOWNSTREAM tRNA:M-i:61D INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi
3R	25758849	3R_25758849_SNP [dm3] 3R_29933127_SNP [dm6]	T	A	4.740e^-5	0.978	UPSTREAM CG42557 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	10925619	2R_10925619_SNP [dm3] 2R_15038114_SNP [dm6]	A	G	4.748e^-5	0.978	INTRON hbs
X	6477066	X_6477066_SNP [dm3] X_6583033_SNP [dm6]	A	G	4.759e^-5	0.978	SYNONYMOUS_CODING CG34417 INTRON CG34417
3L	2644981	3L_2644981_SNP [dm3] 3L_2644981_SNP [dm6]	A	T	4.774e^-5	0.978	UPSTREAM CG1143 INTERGENIC
2R	9147482	2R_9147482_SNP [dm3] 2R_13259977_SNP [dm6]	A	G	4.807e^-5	0.978	UPSTREAM CG42319 INTERGENIC
3L	12147000	3L_12147000_SNP [dm3] 3L_12153900_SNP [dm6]	C	T	4.814e^-5	0.978	INTRON Nrx-IV
X	6216324	X_6216324_SNP [dm3] X_6322291_SNP [dm6]	G	A	5.000e^-5	0.978	INTRON CG15894
3L	4534444	3L_4534444_SNP [dm3] 3L_4534444_SNP [dm6]	C	A	5.069e^-5	0.978	INTRON CG11353
X	12929562	X_12929562_SNP [dm3] X_13035529_SNP [dm6]	T	A	5.090e^-5	0.978	INTRON rad
2L	8986559	2L_8986559_SNP [dm3] 2L_8986559_SNP [dm6]	T	C	5.168e^-5	0.978	INTRON rost
2L	8986560	2L_8986560_SNP [dm3] 2L_8986560_SNP [dm6]	C	A	5.168e^-5	0.978	INTRON rost
3L	15206488	3L_15206488_SNP [dm3] 3L_15213388_SNP [dm6]	G	T	5.172e^-5	0.978	INTERGENIC
3R	5145048	3R_5145048_SNP [dm3] 3R_9319326_SNP [dm6]	G	A	5.183e^-5	0.978	INTRON CG8861
3L	8582618	3L_8582618_SNP [dm3] 3L_8589518_SNP [dm6]	T	C	5.203e^-5	0.978	UPSTREAM CG43078 INTRON CG43078
2L	8167858	2L_8167858_SNP [dm3] 2L_8167858_SNP [dm6]	G	C	5.204e^-5	0.978	INTRON Piezo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	12600147	X_12600147_SNP [dm3] X_12706114_SNP [dm6]	C	A	5.235e^-5	0.978	UTR_5_PRIME CG15725 INTRON Smr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18831086	X_18831086_SNP [dm3] X_18937053_SNP [dm6]	C	G	5.305e^-5	0.978	INTRON CG43759	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	11981518	3R_11981518_SNP [dm3] 3R_16155796_SNP [dm6]	G	C	5.352e^-5	0.978	INTRON CG6006	TF binding site mE1_TFBS_cad
2R	9131372	2R_9131372_SNP [dm3] 2R_13243867_SNP [dm6]	T	C	5.388e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
2R	12821148	2R_12821148_SNP [dm3] 2R_16933643_SNP [dm6]	C	T	5.531e^-5	0.978	INTRON Pkc53E	TF binding site BDTNP1_TFBS_twi
3L	1561196	3L_1561196_SNP [dm3] 3L_1561196_SNP [dm6]	G	T	5.585e^-5	0.978	NON_SYNONYMOUS_CODING CG7879	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	7291366	3L_7291366_SNP [dm3] 3L_7298266_SNP [dm6]	G	C	5.622e^-5	0.978	INTRON unc-13-4A
2R	11330066	2R_11330066_SNP [dm3] 2R_15442561_SNP [dm6]	G	T	5.693e^-5	0.978	INTRON CG43729
2L	10085825	2L_10085825_SNP [dm3] 2L_10085825_SNP [dm6]	C	T	5.784e^-5	0.978	INTRON CG44153
2R	9131360	2R_9131360_SNP [dm3] 2R_13243855_SNP [dm6]	C	T	5.817e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC
3L	16983323	3L_16983323_SNP [dm3] 3L_16990223_SNP [dm6]	A	G	5.901e^-5	0.978	INTRON Exn
2L	8697403	2L_8697403_SNP [dm3] 2L_8697403_SNP [dm6]	T	G	5.957e^-5	0.978	INTRON Hnf4
2R	19297196	2R_19297196_SNP [dm3] 2R_23409673_SNP [dm6]	C	G	5.998e^-5	0.978	INTERGENIC
3L	1066558	3L_1066558_SNP [dm3] 3L_1066558_SNP [dm6]	C	G	6.024e^-5	0.978	INTRON bab1
3L	1172112	3L_1172112_SNP [dm3] 3L_1172112_SNP [dm6]	C	G	6.112e^-5	0.978	INTRON bab2	regulatory region REDfly_CRMs
X	12190729	X_12190729_SNP [dm3] X_12296696_SNP [dm6]	G	A	6.129e^-5	0.978	INTRON Ten-a
3L	8908321	3L_8908321_SNP [dm3] 3L_8915221_SNP [dm6]	C	T	6.147e^-5	0.978	UPSTREAM CR43970 INTRON Tsp66E
3L	2646310	3L_2646310_SNP [dm3] 3L_2646310_SNP [dm6]	T	C	6.189e^-5	0.978	SYNONYMOUS_CODING CG1143	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9131320	2R_9131320_SNP [dm3] 2R_13243815_SNP [dm6]	T	G	6.251e^-5	0.978	DOWNSTREAM CR45278 INTERGENIC

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By genomic position
Variant impact
Gene name

Wing_L5_Vein_Length phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results