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=6.306e^-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_3R_K	0.06308

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1840 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
3R	26752160	3R_26752160_SNP [dm3] 3R_30926438_SNP [dm6]	G	T	1.348e^-6	0.946	INTRON Ptx1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi
2R	12131857	2R_12131857_SNP [dm3] 2R_16244352_SNP [dm6]	T	A	3.118e^-6	0.946	INTRON CngA	TF binding site mE1_TFBS_inv
2L	3693283	2L_3693283_SNP [dm3] 2L_3693283_SNP [dm6]	T	G	6.535e^-6	0.946	UTR_3_PRIME Acp24A4 UPSTREAM CG16704 & 1 other DOWNSTREAM Acp24A4 & 1 other
3L	9291423	3L_9291423_SNP [dm3] 3L_9298323_SNP [dm6]	T	C	6.614e^-6	0.946	INTERGENIC
X	555398	X_555398_SNP [dm3] X_661365_SNP [dm6]	C	G	8.816e^-6	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	3512030	2R_3512030_SNP [dm3] 2R_7624525_SNP [dm6]	A	C	9.794e^-6	0.946	INTRON CG43340
3R	23230851	3R_23230851_SNP [dm3] 3R_27405129_SNP [dm6]	C	T	9.865e^-6	0.946	INTRON side
2R	16131320	2R_16131320_SNP [dm3] 2R_20243815_SNP [dm6]	G	A	1.005e^-5	0.946	NON_SYNONYMOUS_CODING CG11208 DOWNSTREAM Efhc1.2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	19501983	2R_19501983_SNP [dm3] 2R_23614460_SNP [dm6]	C	T	1.034e^-5	0.946	INTRON CG17664 & 1 other	TF binding site BDTNP1_TFBS_dl
2R	16130908	2R_16130908_SNP [dm3] 2R_20243403_SNP [dm6]	A	T	1.149e^-5	0.946	SYNONYMOUS_CODING CG11208 DOWNSTREAM Efhc1.2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
3L	18901900	3L_18901900_SNP [dm3] 3L_18908800_SNP [dm6]	A	C	1.180e^-5	0.946	UTR_3_PRIME CG6841 INTRON CG14077 & 1 other	TF binding site mE1_TFBS_cad
2R	9883267	2R_9883267_SNP [dm3] 2R_13995762_SNP [dm6]	G	A	1.203e^-5	0.946	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	11439716	3R_11439716_SNP [dm3] 3R_15613994_SNP [dm6]	A	G	1.238e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_Kr
3L	10920622	3L_10920622_SNP [dm3] 3L_10927522_SNP [dm6]	T	G	1.251e^-5	0.946	INTERGENIC
2L	8037802	2L_8037802_SNP [dm3] 2L_8037802_SNP [dm6]	G	A	1.475e^-5	0.946	SYNONYMOUS_CODING Cka INTRON CG7367	TF binding site mE1_TFBS_sens
2R	12333720	2R_12333720_SNP [dm3] 2R_16446215_SNP [dm6]	T	A	1.569e^-5	0.946	UTR_5_PRIME CG15925
3L	12503800	3L_12503800_SNP [dm3] 3L_12510700_SNP [dm6]	A	C	1.574e^-5	0.946	NON_SYNONYMOUS_CODING sti
3L	18127102	3L_18127102_SNP [dm3] 3L_18134002_SNP [dm6]	C	T	1.612e^-5	0.946	INTERGENIC
X	6518634	X_6518634_SNP [dm3] X_6624601_SNP [dm6]	C	T	1.642e^-5	0.946	INTRON pigs	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3R	14444206	3R_14444206_SNP [dm3] 3R_18618484_SNP [dm6]	G	T	1.652e^-5	0.946	UPSTREAM CG7695 INTRON qin & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	16130617	2R_16130617_SNP [dm3] 2R_20243112_SNP [dm6]	G	T	1.723e^-5	0.946	DOWNSTREAM Efhc1.2 INTRON CG11208	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	8622171	X_8622171_SNP [dm3] X_8728138_SNP [dm6]	C	A	1.842e^-5	0.946	INTERGENIC
3L	8651680	3L_8651680_SNP [dm3] 3L_8658580_SNP [dm6]	G	A	1.884e^-5	0.946	INTERGENIC
3L	15420539	3L_15420539_SNP [dm3] 3L_15427439_SNP [dm6]	T	A	1.988e^-5	0.946	INTERGENIC
X	21471217	X_21471217_SNP [dm3] X_21600190_SNP [dm6]	A	G	2.037e^-5	0.946	DOWNSTREAM CG14476 INTERGENIC
3L	10628517	3L_10628517_SNP [dm3] 3L_10635417_SNP [dm6]	C	T	2.065e^-5	0.946	SYNONYMOUS_CODING E_z_ DOWNSTREAM CG34001
2R	20183896	2R_20183896_SNP [dm3] 2R_24296373_SNP [dm6]	G	A	2.093e^-5	0.946	SYNONYMOUS_CODING CG3394	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	8651688	3L_8651688_SNP [dm3] 3L_8658588_SNP [dm6]	A	C	2.098e^-5	0.946	INTERGENIC
3R	24100340	3R_24100340_SNP [dm3] 3R_28274618_SNP [dm6]	C	A	2.210e^-5	0.946	INTERGENIC
3L	18897412	3L_18897412_SNP [dm3] 3L_18904312_SNP [dm6]	T	G	2.322e^-5	0.946	SYNONYMOUS_CODING CSN1b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	2995056	3L_2995056_SNP [dm3] 3L_2995056_SNP [dm6]	T	C	2.439e^-5	0.946	UPSTREAM CG2113 INTERGENIC
3R	24100324	3R_24100324_SNP [dm3] 3R_28274602_SNP [dm6]	A	T	2.458e^-5	0.946	INTERGENIC
3L	9034005	3L_9034005_SNP [dm3] 3L_9040905_SNP [dm6]	C	A	2.506e^-5	0.946	UPSTREAM Doc1 INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	18897058	3L_18897058_SNP [dm3] 3L_18903958_SNP [dm6]	G	A	2.519e^-5	0.946	SYNONYMOUS_CODING CSN1b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	6738690	2L_6738690_SNP [dm3] 2L_6738690_SNP [dm6]	T	C	2.525e^-5	0.946	INTRON TTLL3A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
X	2362060	X_2362060_SNP [dm3] X_2468027_SNP [dm6]	A	T	2.633e^-5	0.946	INTRON boi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	3693285	2L_3693285_SNP [dm3] 2L_3693285_SNP [dm6]	T	C	2.651e^-5	0.946	UTR_3_PRIME Acp24A4 UPSTREAM CG16704 & 1 other DOWNSTREAM Acp24A4 & 1 other
3L	5191651	3L_5191651_SNP [dm3] 3L_5198551_SNP [dm6]	G	A	2.767e^-5	0.946	INTRON shep
X	5891600	X_5891600_SNP [dm3] X_5997567_SNP [dm6]	T	C	2.780e^-5	0.946	UTR_3_PRIME CG4766	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18898485	3L_18898485_SNP [dm3] 3L_18905385_SNP [dm6]	T	C	2.788e^-5	0.946	UTR_5_PRIME CG6841 UPSTREAM CSN1b
3R	14444033	3R_14444033_SNP [dm3] 3R_18618311_SNP [dm6]	A	G	2.830e^-5	0.946	UPSTREAM CG7695 INTRON qin & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	1560977	3L_1560977_SNP [dm3] 3L_1560977_SNP [dm6]	G	A	2.835e^-5	0.946	NON_SYNONYMOUS_CODING CG7879	TF binding site BDTNP1_TFBS_da
3R	18184751	3R_18184751_SNP [dm3] 3R_22359029_SNP [dm6]	T	A	2.970e^-5	0.946	INTRON Sar1
3R	15164335	3R_15164335_SNP [dm3] 3R_19338613_SNP [dm6]	A	T	3.011e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	7663519	X_7663519_SNP [dm3] X_7769486_SNP [dm6]	G	C	3.045e^-5	0.946	DOWNSTREAM CG34338 INTERGENIC
2R	19663848	2R_19663848_SNP [dm3] 2R_23776325_SNP [dm6]	T	G	3.173e^-5	0.946	INTRON CG9850
2R	13059677	2R_13059677_DEL [dm3] 2R_17172172_DEL [dm6]	GGTATTTTGGC...	G	3.224e^-5	0.946	INTERGENIC
X	11185285	X_11185285_SNP [dm3] X_11291252_SNP [dm6]	G	A	3.259e^-5	0.946	INTRON CG44422
X	1783119	X_1783119_SNP [dm3] X_1889086_SNP [dm6]	T	G	3.397e^-5	0.946	SYNONYMOUS_CODING trr	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	6220596	3R_6220596_SNP [dm3] 3R_10394874_SNP [dm6]	C	T	3.553e^-5	0.946	INTRON cwo
3L	8651870	3L_8651870_SNP [dm3] 3L_8658770_SNP [dm6]	G	A	3.707e^-5	0.946	INTERGENIC
3L	12125004	3L_12125004_SNP [dm3] 3L_12131904_SNP [dm6]	T	A	3.739e^-5	0.946	UPSTREAM CG11534 DOWNSTREAM Lsp2 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna mE1_TFBS_HSA
X	9795080	X_9795080_SNP [dm3] X_9901047_SNP [dm6]	G	A	3.820e^-5	0.946	INTERGENIC
2R	3429018	2R_3429018_SNP [dm3] 2R_7541513_SNP [dm6]	C	A	3.984e^-5	0.946	INTRON Corin
2R	3429218	2R_3429218_SNP [dm3] 2R_7541713_SNP [dm6]	C	T	3.984e^-5	0.946	INTRON Corin
2R	3429763	2R_3429763_SNP [dm3] 2R_7542258_SNP [dm6]	G	A	3.984e^-5	0.946	INTRON Corin
2R	3431865	2R_3431865_SNP [dm3] 2R_7544360_SNP [dm6]	T	A	3.984e^-5	0.946	UPSTREAM Corin INTRON Corin	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	3433484	2R_3433484_SNP [dm3] 2R_7545979_SNP [dm6]	T	C	3.984e^-5	0.946	START_GAINED Corin UTR_5_PRIME Corin INTRON Corin
2R	3432923	2R_3432923_SNP [dm3] 2R_7545418_SNP [dm6]	T	C	4.039e^-5	0.946	UTR_5_PRIME Corin INTRON Corin	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	15020334	2L_15020334_SNP [dm3] 2L_15020334_SNP [dm6]	C	T	4.096e^-5	0.946	INTRON GABA-B-R1
2R	3431923	2R_3431923_SNP [dm3] 2R_7544418_SNP [dm6]	A	C	4.175e^-5	0.946	UPSTREAM Corin INTRON Corin	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	9037791	3L_9037791_SNP [dm3] 3L_9044691_SNP [dm6]	C	A	4.342e^-5	0.946	NON_SYNONYMOUS_CODING Doc1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	3432108	2R_3432108_SNP [dm3] 2R_7544603_SNP [dm6]	C	A	4.380e^-5	0.946	UPSTREAM Corin INTRON Corin	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	11185349	X_11185349_SNP [dm3] X_11291316_SNP [dm6]	C	T	4.383e^-5	0.946	INTRON CG44422
3L	4318164	3L_4318164_SNP [dm3] 3L_4318164_SNP [dm6]	C	T	4.471e^-5	0.946	SYNONYMOUS_CODING Claspin UPSTREAM CG32250	TF binding site mE1_TFBS_HSA
3L	15022643	3L_15022643_SNP [dm3] 3L_15029543_SNP [dm6]	G	T	4.500e^-5	0.946	INTRON Sytbeta
3L	9291483	3L_9291483_SNP [dm3] 3L_9298383_SNP [dm6]	A	T	4.519e^-5	0.946	INTERGENIC
3L	9291486	3L_9291486_MNP [dm3] 3L_9298386_MNP [dm6]	GGC	TCA	4.519e^-5	0.946	INTERGENIC
3R	23546658	3R_23546658_SNP [dm3] 3R_27720936_SNP [dm6]	C	T	4.543e^-5	0.946	INTERGENIC
X	4376305	X_4376305_SNP [dm3] X_4482272_SNP [dm6]	T	C	4.574e^-5	0.946	SYNONYMOUS_CODING bi INTRON CR32773
X	574558	X_574558_SNP [dm3] X_680525_SNP [dm6]	G	C	4.582e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	3425376	2R_3425376_SNP [dm3] 2R_7537871_SNP [dm6]	T	C	4.674e^-5	0.946	SYNONYMOUS_CODING CG2137 DOWNSTREAM CG1598	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15164315	3R_15164315_SNP [dm3] 3R_19338593_SNP [dm6]	G	C	4.842e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	10185502	2L_10185502_SNP [dm3] 2L_10185502_SNP [dm6]	A	G	4.879e^-5	0.946	INTRON Sur
2L	12445302	2L_12445302_SNP [dm3] 2L_12445302_SNP [dm6]	G	C	4.897e^-5	0.946	DOWNSTREAM CG5421 INTRON Oatp33Ea	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	555157	X_555157_SNP [dm3] X_661124_SNP [dm6]	T	A	4.922e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15164351	3R_15164351_SNP [dm3] 3R_19338629_SNP [dm6]	A	T	4.940e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	5774556	3R_5774556_INS [dm3] 3R_9948834_INS [dm6]	T	TTCAGCT	5.019e^-5	0.946	INTRON Glut4EF
3L	18897328	3L_18897328_SNP [dm3] 3L_18904228_SNP [dm6]	G	A	5.241e^-5	0.946	SYNONYMOUS_CODING CSN1b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	24100342	3R_24100342_SNP [dm3] 3R_28274620_SNP [dm6]	C	T	5.267e^-5	0.946	INTERGENIC
3R	15164353	3R_15164353_SNP [dm3] 3R_19338631_SNP [dm6]	G	A	5.356e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	18184732	3R_18184732_SNP [dm3] 3R_22359010_SNP [dm6]	G	A	5.365e^-5	0.946	INTRON Sar1
3L	15278056	3L_15278056_SNP [dm3] 3L_15284956_SNP [dm6]	A	G	5.421e^-5	0.946	INTERGENIC
3L	12888102	3L_12888102_INS [dm3] 3L_12895002_INS [dm6]	G	GTCG	5.504e^-5	0.946	DOWNSTREAM CG14118 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	20135541	2L_20135541_SNP [dm3] 2L_20135541_SNP [dm6]	A	C	5.553e^-5	0.946	UPSTREAM CG10651 INTERGENIC
3R	15680094	3R_15680094_SNP [dm3] 3R_19854372_SNP [dm6]	T	A	5.560e^-5	0.946	UTR_3_PRIME CG4662 & 1 other DOWNSTREAM CG4662	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sbb
2L	9460389	2L_9460389_SNP [dm3] 2L_9460389_SNP [dm6]	G	C	5.561e^-5	0.946	INTRON numb	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	12131858	2R_12131858_SNP [dm3] 2R_16244353_SNP [dm6]	A	T	5.569e^-5	0.946	INTRON CngA	TF binding site mE1_TFBS_inv
3L	4291273	3L_4291273_SNP [dm3] 3L_4291273_SNP [dm6]	T	A	5.755e^-5	0.946	UTR_3_PRIME CG15012 DOWNSTREAM Hexo1
3R	26189151	3R_26189151_SNP [dm3] 3R_30363429_SNP [dm6]	A	G	5.809e^-5	0.946	UTR_3_PRIME hdc
3R	24100336	3R_24100336_SNP [dm3] 3R_28274614_SNP [dm6]	C	A	5.816e^-5	0.946	INTERGENIC
3R	24100366	3R_24100366_DEL [dm3] 3R_28274644_DEL [dm6]	ATAA	A	5.822e^-5	0.946	INTERGENIC
3L	1560975	3L_1560975_SNP [dm3] 3L_1560975_SNP [dm6]	G	T	5.847e^-5	0.946	SYNONYMOUS_CODING CG7879	TF binding site BDTNP1_TFBS_da
2L	1344305	2L_1344305_SNP [dm3] 2L_1344305_SNP [dm6]	G	T	5.958e^-5	0.946	UPSTREAM Cdlc2 & 1 other INTERGENIC
3R	26429714	3R_26429714_SNP [dm3] 3R_30603992_SNP [dm6]	C	A	5.977e^-5	0.946	UTR_3_PRIME CG31021 UPSTREAM PH4alphaNE3
X	17324201	X_17324201_SNP [dm3] X_17430168_SNP [dm6]	T	C	6.062e^-5	0.946	INTRON CG12994
3R	10983276	3R_10983276_SNP [dm3] 3R_15157554_SNP [dm6]	T	A	6.178e^-5	0.946	INTRON Gyc88E
3L	11867256	3L_11867256_SNP [dm3] 3L_11874156_SNP [dm6]	C	T	6.215e^-5	0.946	INTRON CG44837
X	570113	X_570113_SNP [dm3] X_676080_SNP [dm6]	A	G	6.398e^-5	0.946	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3R	22010133	3R_22010133_SNP [dm3] 3R_26184411_SNP [dm6]	A	T	6.445e^-5	0.946	SPLICE_SITE_REGION CG31323 UPSTREAM CG31086 INTRON CG31323	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna 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=9.454e^-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_3R_K	0.03968

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	6.5751	0.0373

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1787 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
2R	12131857	2R_12131857_SNP [dm3] 2R_16244352_SNP [dm6]	T	A	5.356e^-7	0.976	INTRON CngA	TF binding site mE1_TFBS_inv
3L	18897412	3L_18897412_SNP [dm3] 3L_18904312_SNP [dm6]	T	G	1.235e^-6	0.976	SYNONYMOUS_CODING CSN1b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	15020334	2L_15020334_SNP [dm3] 2L_15020334_SNP [dm6]	C	T	1.591e^-6	0.976	INTRON GABA-B-R1
3L	18898485	3L_18898485_SNP [dm3] 3L_18905385_SNP [dm6]	T	C	2.585e^-6	0.976	UTR_5_PRIME CG6841 UPSTREAM CSN1b
3L	18897058	3L_18897058_SNP [dm3] 3L_18903958_SNP [dm6]	G	A	3.426e^-6	0.976	SYNONYMOUS_CODING CSN1b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	19501983	2R_19501983_SNP [dm3] 2R_23614460_SNP [dm6]	C	T	4.173e^-6	0.976	INTRON CG17664 & 1 other	TF binding site BDTNP1_TFBS_dl
3L	8383762	3L_8383762_SNP [dm3] 3L_8390662_SNP [dm6]	A	G	4.727e^-6	0.976	UTR_3_PRIME ImpE1 UPSTREAM Jon66Ci
3L	4318164	3L_4318164_SNP [dm3] 3L_4318164_SNP [dm6]	C	T	5.108e^-6	0.976	SYNONYMOUS_CODING Claspin UPSTREAM CG32250	TF binding site mE1_TFBS_HSA
3L	10852580	3L_10852580_INS [dm3] 3L_10859480_INS [dm6]	T	TAT	5.300e^-6	0.976	INTRON tna	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_kn mE1_TFBS_sbb
3L	18897328	3L_18897328_SNP [dm3] 3L_18904228_SNP [dm6]	G	A	5.427e^-6	0.976	SYNONYMOUS_CODING CSN1b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	18901900	3L_18901900_SNP [dm3] 3L_18908800_SNP [dm6]	A	C	5.807e^-6	0.976	UTR_3_PRIME CG6841 INTRON CG14077 & 1 other	TF binding site mE1_TFBS_cad
3L	18897364	3L_18897364_SNP [dm3] 3L_18904264_SNP [dm6]	C	T	9.422e^-6	0.976	SYNONYMOUS_CODING CSN1b	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	2362060	X_2362060_SNP [dm3] X_2468027_SNP [dm6]	A	T	9.659e^-6	0.976	INTRON boi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	18880123	3R_18880123_SNP [dm3] 3R_23054401_SNP [dm6]	G	A	9.671e^-6	0.976	UPSTREAM p53 DOWNSTREAM CG17119 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Ubx
3R	14444206	3R_14444206_SNP [dm3] 3R_18618484_SNP [dm6]	G	T	9.685e^-6	0.976	UPSTREAM CG7695 INTRON qin & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	17934562	3L_17934562_SNP [dm3] 3L_17941462_SNP [dm6]	C	T	1.429e^-5	0.976	INTRON CG43174
X	7663519	X_7663519_SNP [dm3] X_7769486_SNP [dm6]	G	C	1.440e^-5	0.976	DOWNSTREAM CG34338 INTERGENIC
2R	13059677	2R_13059677_DEL [dm3] 2R_17172172_DEL [dm6]	GGTATTTTGGC...	G	1.482e^-5	0.976	INTERGENIC
2R	9883267	2R_9883267_SNP [dm3] 2R_13995762_SNP [dm6]	G	A	1.502e^-5	0.976	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	8037802	2L_8037802_SNP [dm3] 2L_8037802_SNP [dm6]	G	A	1.530e^-5	0.976	SYNONYMOUS_CODING Cka INTRON CG7367	TF binding site mE1_TFBS_sens
X	21384446	X_21384446_SNP [dm3] X_21513419_SNP [dm6]	T	C	1.620e^-5	0.976	INTRON CR45082
2L	14569611	2L_14569611_SNP [dm3] 2L_14569611_SNP [dm6]	C	T	1.669e^-5	0.976	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	18897526	3L_18897526_SNP [dm3] 3L_18904426_SNP [dm6]	C	T	1.715e^-5	0.976	SYNONYMOUS_CODING CSN1b UPSTREAM CG6841	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	18897858	3L_18897858_SNP [dm3] 3L_18904758_SNP [dm6]	T	C	1.900e^-5	0.976	UPSTREAM CG6841 INTRON CSN1b	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2R	20183896	2R_20183896_SNP [dm3] 2R_24296373_SNP [dm6]	G	A	1.932e^-5	0.976	SYNONYMOUS_CODING CG3394	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	13400561	3L_13400561_SNP [dm3] 3L_13407461_SNP [dm6]	A	T	2.039e^-5	0.976	INTERGENIC	TF binding site mE1_TFBS_cad
2L	13996948	2L_13996948_SNP [dm3] 2L_13996948_SNP [dm6]	T	C	2.068e^-5	0.976	INTRON rk
2R	6141472	2R_6141472_SNP [dm3] 2R_10253967_SNP [dm6]	C	T	2.106e^-5	0.976	SYNONYMOUS_CODING CG12913	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	12125004	3L_12125004_SNP [dm3] 3L_12131904_SNP [dm6]	T	A	2.171e^-5	0.976	UPSTREAM CG11534 DOWNSTREAM Lsp2 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna mE1_TFBS_HSA
X	21384283	X_21384283_SNP [dm3] X_21513256_SNP [dm6]	A	G	2.209e^-5	0.976	INTRON CR45082
3R	19536461	3R_19536461_SNP [dm3] 3R_23710739_SNP [dm6]	T	C	2.281e^-5	0.976	SYNONYMOUS_CODING CG10301 UPSTREAM CG10300
3R	16004116	3R_16004116_INS [dm3] 3R_20178394_INS [dm6]	C	CTGGATCCTC	2.491e^-5	0.976	INTERGENIC
3L	18897932	3L_18897932_INS [dm3] 3L_18904832_INS [dm6]	A	AC	2.799e^-5	0.976	UTR_5_PRIME CSN1b UPSTREAM CG6841	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3L	12986194	3L_12986194_SNP [dm3] 3L_12993094_SNP [dm6]	A	T	2.915e^-5	0.976	INTERGENIC
3L	1254840	3L_1254840_SNP [dm3] 3L_1254840_SNP [dm6]	C	A	3.091e^-5	0.976	SYNONYMOUS_CODING CG9133 UTR_3_PRIME CG9130	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	12986198	3L_12986198_SNP [dm3] 3L_12993098_SNP [dm6]	T	A	3.097e^-5	0.976	INTERGENIC
3R	18591051	3R_18591051_SNP [dm3] 3R_22765329_SNP [dm6]	A	G	3.141e^-5	0.976	SYNONYMOUS_CODING CG4721 INTRON Usp12-46 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	14456794	3L_14456794_SNP [dm3] 3L_14463694_SNP [dm6]	A	T	3.186e^-5	0.976	INTRON bbg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13400560	3L_13400560_SNP [dm3] 3L_13407460_SNP [dm6]	G	C	3.390e^-5	0.976	INTERGENIC	TF binding site mE1_TFBS_cad
3L	12986197	3L_12986197_SNP [dm3] 3L_12993097_SNP [dm6]	A	T	3.550e^-5	0.976	INTERGENIC
2L	8330528	2L_8330528_SNP [dm3] 2L_8330528_SNP [dm6]	A	G	3.552e^-5	0.976	INTRON CG14275
3L	18898719	3L_18898719_INS [dm3] 3L_18905619_INS [dm6]	A	ATCTACC	3.581e^-5	0.976	UPSTREAM CSN1b INTRON CG6841	TF binding site mE1_TFBS_cad
3L	18898724	3L_18898724_SNP [dm3] 3L_18905624_SNP [dm6]	A	G	3.581e^-5	0.976	UPSTREAM CSN1b INTRON CG6841	TF binding site mE1_TFBS_cad
3L	18898377	3L_18898377_SNP [dm3] 3L_18905277_SNP [dm6]	T	G	3.587e^-5	0.976	UPSTREAM CG6841 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	16131320	2R_16131320_SNP [dm3] 2R_20243815_SNP [dm6]	G	A	3.660e^-5	0.976	NON_SYNONYMOUS_CODING CG11208 DOWNSTREAM Efhc1.2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	18858554	2R_18858554_DEL [dm3] 2R_22971031_DEL [dm6]	GA	G	3.778e^-5	0.976	INTERGENIC
3L	12986181	3L_12986181_SNP [dm3] 3L_12993081_SNP [dm6]	G	C	3.864e^-5	0.976	INTERGENIC
X	9465442	X_9465442_SNP [dm3] X_9571409_SNP [dm6]	C	A	3.924e^-5	0.976	UPSTREAM Cubn DOWNSTREAM CG32699 INTERGENIC
3L	10445277	3L_10445277_SNP [dm3] 3L_10452177_SNP [dm6]	A	C	3.948e^-5	0.976	INTERGENIC
3L	12986173	3L_12986173_SNP [dm3] 3L_12993073_SNP [dm6]	G	T	3.954e^-5	0.976	INTERGENIC
3R	17883389	3R_17883389_SNP [dm3] 3R_22057667_SNP [dm6]	A	G	4.026e^-5	0.976	INTRON how	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	26752160	3R_26752160_SNP [dm3] 3R_30926438_SNP [dm6]	G	T	4.050e^-5	0.976	INTRON Ptx1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi
3R	18880135	3R_18880135_SNP [dm3] 3R_23054413_SNP [dm6]	C	T	4.166e^-5	0.976	UTR_3_PRIME CG17119 UPSTREAM p53	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_Ubx
3L	12986166	3L_12986166_SNP [dm3] 3L_12993066_SNP [dm6]	T	A	4.226e^-5	0.976	INTERGENIC
3L	10920622	3L_10920622_SNP [dm3] 3L_10927522_SNP [dm6]	T	G	4.266e^-5	0.976	INTERGENIC
3R	10936643	3R_10936643_SNP [dm3] 3R_15110921_SNP [dm6]	T	C	4.629e^-5	0.976	INTRON CG42788
3L	18875409	3L_18875409_SNP [dm3] 3L_18882309_SNP [dm6]	A	G	4.816e^-5	0.976	INTRON CG3961
3L	12569553	3L_12569553_SNP [dm3] 3L_12576453_SNP [dm6]	G	A	4.919e^-5	0.976	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_kn
2L	1641557	2L_1641557_SNP [dm3] 2L_1641557_SNP [dm6]	A	G	4.940e^-5	0.976	INTERGENIC
3R	14040915	3R_14040915_SNP [dm3] 3R_18215193_SNP [dm6]	A	G	5.002e^-5	0.976	UPSTREAM CG14314 DOWNSTREAM CG7985 INTERGENIC	transposable element FlyBase
X	17324201	X_17324201_SNP [dm3] X_17430168_SNP [dm6]	T	C	5.061e^-5	0.976	INTRON CG12994
3R	14159734	3R_14159734_SNP [dm3] 3R_18334012_SNP [dm6]	T	C	5.205e^-5	0.976	UTR_3_PRIME CG15803
2L	13913327	2L_13913327_DEL [dm3] 2L_13913327_DEL [dm6]	ATTGA	A	5.236e^-5	0.976	DOWNSTREAM Acyp INTERGENIC	TF binding site mE1_TFBS_cad
3R	18483257	3R_18483257_SNP [dm3] 3R_22657535_SNP [dm6]	G	A	5.400e^-5	0.976	INTRON CG45058
3L	1913713	3L_1913713_SNP [dm3] 3L_1913713_SNP [dm6]	C	T	5.538e^-5	0.976	INTERGENIC
3L	1913660	3L_1913660_SNP [dm3] 3L_1913660_SNP [dm6]	T	A	5.596e^-5	0.976	INTERGENIC
X	16775012	X_16775012_SNP [dm3] X_16880979_SNP [dm6]	A	G	5.623e^-5	0.976	UPSTREAM CG4872 INTERGENIC
3L	3135861	3L_3135861_SNP [dm3] 3L_3135861_SNP [dm6]	C	T	5.653e^-5	0.976	INTRON CG11537
X	8192518	X_8192518_SNP [dm3] X_8298485_SNP [dm6]	G	A	5.732e^-5	0.976	INTRON nAChRalpha3
3R	23178817	3R_23178817_SNP [dm3] 3R_27353095_SNP [dm6]	G	A	5.751e^-5	0.976	INTRON CG42534
X	5879487	X_5879487_SNP [dm3] X_5985454_SNP [dm6]	A	C	5.884e^-5	0.976	INTRON Grip
X	11280678	X_11280678_SNP [dm3] X_11386645_SNP [dm6]	T	A	5.962e^-5	0.976	INTRON dlg1
3L	16531305	3L_16531305_SNP [dm3] 3L_16538205_SNP [dm6]	C	T	5.985e^-5	0.976	INTRON CG43373
3L	1913735	3L_1913735_SNP [dm3] 3L_1913735_SNP [dm6]	A	G	6.040e^-5	0.976	INTERGENIC
3L	12986142	3L_12986142_SNP [dm3] 3L_12993042_SNP [dm6]	T	C	6.090e^-5	0.976	INTERGENIC
3R	18581576	3R_18581576_SNP [dm3] 3R_22755854_SNP [dm6]	T	C	6.162e^-5	0.976	INTRON Usp12-46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	1707019	2L_1707019_SNP [dm3] 2L_1707019_SNP [dm6]	A	T	6.163e^-5	0.976	DOWNSTREAM CG17660 & 1 other INTERGENIC
3L	17934578	3L_17934578_SNP [dm3] 3L_17941478_SNP [dm6]	C	T	6.254e^-5	0.976	INTRON CG43174	TF binding site mE1_TFBS_HSA
3R	26189151	3R_26189151_SNP [dm3] 3R_30363429_SNP [dm6]	A	G	6.281e^-5	0.976	UTR_3_PRIME hdc
3L	17454584	3L_17454584_SNP [dm3] 3L_17461484_SNP [dm6]	G	A	6.350e^-5	0.976	DOWNSTREAM CR44565 INTERGENIC
3R	9706320	3R_9706320_DEL [dm3] 3R_13880598_DEL [dm6]	ACAAATGGCCAGCAAAATGC...	A	6.510e^-5	0.976	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3L	12986144	3L_12986144_SNP [dm3] 3L_12993044_SNP [dm6]	A	G	6.604e^-5	0.976	INTERGENIC
3L	10846870	3L_10846870_SNP [dm3] 3L_10853770_SNP [dm6]	C	G	6.701e^-5	0.976	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	1707024	2L_1707024_SNP [dm3] 2L_1707024_SNP [dm6]	A	T	6.715e^-5	0.976	DOWNSTREAM CG17660 & 1 other INTERGENIC
2R	14879690	2R_14879690_SNP [dm3] 2R_18992185_SNP [dm6]	C	T	6.716e^-5	0.976	INTRON tn
3R	13811326	3R_13811326_SNP [dm3] 3R_17985604_SNP [dm6]	A	T	6.724e^-5	0.976	INTRON cpo
2R	3432923	2R_3432923_SNP [dm3] 2R_7545418_SNP [dm6]	T	C	6.764e^-5	0.976	UTR_5_PRIME Corin INTRON Corin	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	8068491	X_8068491_SNP [dm3] X_8174458_SNP [dm6]	C	T	6.959e^-5	0.976	INTRON slpr
2L	13961300	2L_13961300_SNP [dm3] 2L_13961300_SNP [dm6]	T	C	7.003e^-5	0.976	SYNONYMOUS_CODING NimA	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	11443571	3R_11443571_SNP [dm3] 3R_15617849_SNP [dm6]	A	G	7.011e^-5	0.976	INTERGENIC
2R	3429018	2R_3429018_SNP [dm3] 2R_7541513_SNP [dm6]	C	A	7.053e^-5	0.976	INTRON Corin
2R	3429218	2R_3429218_SNP [dm3] 2R_7541713_SNP [dm6]	C	T	7.053e^-5	0.976	INTRON Corin
2R	3429763	2R_3429763_SNP [dm3] 2R_7542258_SNP [dm6]	G	A	7.053e^-5	0.976	INTRON Corin
2R	3431865	2R_3431865_SNP [dm3] 2R_7544360_SNP [dm6]	T	A	7.053e^-5	0.976	UPSTREAM Corin INTRON Corin	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	3433484	2R_3433484_SNP [dm3] 2R_7545979_SNP [dm6]	T	C	7.053e^-5	0.976	START_GAINED Corin UTR_5_PRIME Corin INTRON Corin
3L	12986207	3L_12986207_SNP [dm3] 3L_12993107_SNP [dm6]	T	C	7.056e^-5	0.976	INTERGENIC
3R	15651069	3R_15651069_SNP [dm3] 3R_19825347_SNP [dm6]	G	A	7.208e^-5	0.976	INTRON bnl
2R	3431923	2R_3431923_SNP [dm3] 2R_7544418_SNP [dm6]	A	C	7.350e^-5	0.976	UPSTREAM Corin INTRON Corin	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	3432108	2R_3432108_SNP [dm3] 2R_7544603_SNP [dm6]	C	A	7.380e^-5	0.976	UPSTREAM Corin INTRON Corin	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	15237280	2R_15237280_SNP [dm3] 2R_19349775_SNP [dm6]	G	A	7.433e^-5	0.976	START_GAINED Rgk1 UTR_5_PRIME Rgk1

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By genomic position
Variant impact
Gene name

pc_Tarsus_Leg_T2 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