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=2.922e^-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_P	0.028149
In_3R_K	0.090770
In_3R_Mo	0.001833

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	6.8861	0.032
In_3R_K	6.9902	0.0303
In_3R_Mo	7.3985	0.0247

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1914 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
X	3422445	X_3422445_SNP [dm3] X_3528412_SNP [dm6]	G	A	1.040e^-6	0.871	INTRON CG32791
X	3422598	X_3422598_SNP [dm3] X_3528565_SNP [dm6]	T	A	1.341e^-6	0.871	INTRON CG32791
3R	10974548	3R_10974548_SNP [dm3] 3R_15148826_SNP [dm6]	T	A	3.235e^-6	0.871	INTERGENIC
2R	14643414	2R_14643414_SNP [dm3] 2R_18755909_SNP [dm6]	A	T	3.476e^-6	0.871	INTRON Cyp12b2
3R	10974560	3R_10974560_SNP [dm3] 3R_15148838_SNP [dm6]	T	C	4.460e^-6	0.871	INTERGENIC
3R	9025755	3R_9025755_SNP [dm3] 3R_13200033_SNP [dm6]	A	T	5.335e^-6	0.871	INTERGENIC
3L	11741814	3L_11741814_SNP [dm3] 3L_11748714_SNP [dm6]	C	T	5.360e^-6	0.871	INTRON CG6024
3R	5963331	3R_5963331_SNP [dm3] 3R_10137609_SNP [dm6]	A	C	6.278e^-6	0.871	INTRON tws	TF binding site mE1_TFBS_bab1
3R	8791257	3R_8791257_SNP [dm3] 3R_12965535_SNP [dm6]	C	T	7.687e^-6	0.871	SYNONYMOUS_CODING Cyp304a1 DOWNSTREAM CG14384 INTRON grsm	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14805308	2R_14805308_SNP [dm3] 2R_18917803_SNP [dm6]	C	T	8.028e^-6	0.871	INTRON sano
3R	6099893	3R_6099893_SNP [dm3] 3R_10274171_SNP [dm6]	G	A	9.014e^-6	0.871	INTRON CG43143
3R	8482294	3R_8482294_INS [dm3] 3R_12656572_INS [dm6]	C	CC	9.018e^-6	0.871	INTRON CG6225
3R	11706259	3R_11706259_SNP [dm3] 3R_15880537_SNP [dm6]	A	T	9.283e^-6	0.871	INTERGENIC
X	918217	X_918217_SNP [dm3] X_1024184_SNP [dm6]	C	A	9.568e^-6	0.871	INTRON su_w[a]_ & 2 others
3R	8788977	3R_8788977_SNP [dm3] 3R_12963255_SNP [dm6]	T	A	1.031e^-5	0.871	UPSTREAM Cyp304a1 DOWNSTREAM Spc25 INTRON grsm
3R	8979781	3R_8979781_SNP [dm3] 3R_13154059_SNP [dm6]	G	A	1.076e^-5	0.871	INTRON timeout & 2 others
3R	25398371	3R_25398371_SNP [dm3] 3R_29572649_SNP [dm6]	A	T	1.156e^-5	0.871	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	2467736	3L_2467736_SNP [dm3] 3L_2467736_SNP [dm6]	A	T	1.163e^-5	0.871	INTRON CG45186	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	6078825	3R_6078825_SNP [dm3] 3R_10253103_SNP [dm6]	C	A	1.198e^-5	0.871	SYNONYMOUS_CODING CG3999
3R	8353992	3R_8353992_SNP [dm3] 3R_12528270_SNP [dm6]	G	T	1.528e^-5	0.871	INTRON Octbeta3R & 1 other
3R	11675976	3R_11675976_SNP [dm3] 3R_15850254_SNP [dm6]	T	A	1.708e^-5	0.871	INTRON cv-d	TF binding site mE1_TFBS_chinmo
3R	11675822	3R_11675822_SNP [dm3] 3R_15850100_SNP [dm6]	G	A	1.821e^-5	0.871	SYNONYMOUS_CODING cv-d	TF binding site mE1_TFBS_chinmo
3R	6087038	3R_6087038_SNP [dm3] 3R_10261316_SNP [dm6]	T	C	1.895e^-5	0.871	NON_SYNONYMOUS_CODING Sirt6 UPSTREAM pont	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	6094882	3R_6094882_SNP [dm3] 3R_10269160_SNP [dm6]	C	T	1.911e^-5	0.871	INTRON CG43143
3R	2253207	3R_2253207_SNP [dm3] 3R_6427485_SNP [dm6]	A	C	1.970e^-5	0.871	INTRON gpp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	6407818	2R_6407818_SNP [dm3] 2R_10520313_SNP [dm6]	A	C	1.989e^-5	0.871	UTR_3_PRIME lola INTRON lola	TF binding site BDTNP1_TFBS_sna
3R	9133366	3R_9133366_SNP [dm3] 3R_13307644_SNP [dm6]	C	T	1.999e^-5	0.871	INTRON CG32473
3R	7711602	3R_7711602_SNP [dm3] 3R_11885880_SNP [dm6]	G	A	1.999e^-5	0.871	INTRON CG31368 & 1 other	TF binding site BDTNP1_TFBS_twi
3L	7290403	3L_7290403_SNP [dm3] 3L_7297303_SNP [dm6]	C	G	2.140e^-5	0.871	INTRON unc-13-4A
X	12207397	X_12207397_INS [dm3] X_12313364_INS [dm6]	C	CGCCAAGTC	2.178e^-5	0.871	INTRON Ten-a
X	920559	X_920559_SNP [dm3] X_1026526_SNP [dm6]	A	G	2.203e^-5	0.871	UTR_5_PRIME CG32814 & 1 other UPSTREAM CG3021 INTRON su_w[a]_	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	14130276	2R_14130276_SNP [dm3] 2R_18242771_SNP [dm6]	C	T	2.209e^-5	0.871	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	11706219	3R_11706219_SNP [dm3] 3R_15880497_SNP [dm6]	T	C	2.578e^-5	0.871	INTERGENIC
3L	12486923	3L_12486923_SNP [dm3] 3L_12493823_SNP [dm6]	C	T	2.626e^-5	0.871	DOWNSTREAM CR45682 INTRON CG10657
3R	9320109	3R_9320109_SNP [dm3] 3R_13494387_SNP [dm6]	A	T	2.659e^-5	0.871	INTERGENIC
3R	9320112	3R_9320112_SNP [dm3] 3R_13494390_SNP [dm6]	G	A	2.659e^-5	0.871	INTERGENIC
3R	8327209	3R_8327209_SNP [dm3] 3R_12501487_SNP [dm6]	G	A	2.721e^-5	0.871	INTERGENIC	transposable element FlyBase
3R	885487	3R_885487_SNP [dm3] 3R_5059765_SNP [dm6]	G	C	2.724e^-5	0.871	INTERGENIC	TF binding site mE1_TFBS_sens
3R	8791530	3R_8791530_SNP [dm3] 3R_12965808_SNP [dm6]	A	C	2.805e^-5	0.871	UTR_3_PRIME Cyp304a1 DOWNSTREAM CG14384 INTRON grsm	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	10698632	3L_10698632_SNP [dm3] 3L_10705532_SNP [dm6]	C	T	3.013e^-5	0.871	INTERGENIC
2R	10897126	2R_10897126_SNP [dm3] 2R_15009621_SNP [dm6]	A	G	3.088e^-5	0.871	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	919050	X_919050_SNP [dm3] X_1025017_SNP [dm6]	C	G	3.103e^-5	0.871	INTRON su_w[a]_ & 2 others	transposable element FlyBase
X	918124	X_918124_SNP [dm3] X_1024091_SNP [dm6]	C	A	3.239e^-5	0.871	INTRON su_w[a]_ & 2 others
3L	2469874	3L_2469874_SNP [dm3] 3L_2469874_SNP [dm6]	T	C	3.313e^-5	0.871	INTRON CG45186	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	11706260	3R_11706260_SNP [dm3] 3R_15880538_SNP [dm6]	C	T	3.335e^-5	0.871	INTERGENIC
2L	15194025	2L_15194025_SNP [dm3] 2L_15194025_SNP [dm6]	T	A	3.436e^-5	0.871	INTRON CG4168
3R	5644403	3R_5644403_SNP [dm3] 3R_9818681_SNP [dm6]	C	T	3.459e^-5	0.871	UPSTREAM CG9459 DOWNSTREAM CG9458 INTERGENIC
3R	8865764	3R_8865764_SNP [dm3] 3R_13040042_SNP [dm6]	A	C	3.477e^-5	0.871	NON_SYNONYMOUS_CODING CG11668 DOWNSTREAM snk
3R	6090694	3R_6090694_SNP [dm3] 3R_10264972_SNP [dm6]	C	T	3.488e^-5	0.871	INTRON CG43143	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	2467964	3L_2467964_SNP [dm3] 3L_2467964_SNP [dm6]	T	G	3.502e^-5	0.871	INTRON CG45186	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_zfh1
3R	6073936	3R_6073936_SNP [dm3] 3R_10248214_SNP [dm6]	G	A	3.538e^-5	0.871	SYNONYMOUS_CODING CG42795	TF binding site mE1_TFBS_inv
2L	12383045	2L_12383045_SNP [dm3] 2L_12383045_SNP [dm6]	C	T	3.636e^-5	0.871	INTRON bru-2
3R	8788982	3R_8788982_SNP [dm3] 3R_12963260_SNP [dm6]	T	A	3.646e^-5	0.871	UPSTREAM Cyp304a1 DOWNSTREAM Spc25 INTRON grsm
3R	25890815	3R_25890815_SNP [dm3] 3R_30065093_SNP [dm6]	C	T	3.666e^-5	0.871	INTRON sima
2R	14646077	2R_14646077_SNP [dm3] 2R_18758572_SNP [dm6]	C	T	3.709e^-5	0.871	SPLICE_SITE_REGION Jabba SYNONYMOUS_CODING Jabba	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	14805328	2R_14805328_SNP [dm3] 2R_18917823_SNP [dm6]	G	T	3.722e^-5	0.871	INTRON sano
2R	1072336	2R_1072336_INS [dm3] 2R_5184831_INS [dm6]	C	CGCC	3.743e^-5	0.871	INTRON Nipped-A
3L	16215923	3L_16215923_SNP [dm3] 3L_16222823_SNP [dm6]	G	A	3.760e^-5	0.871	DOWNSTREAM tRNA:CR32153 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	11918730	3L_11918730_SNP [dm3] 3L_11925630_SNP [dm6]	G	C	3.885e^-5	0.871	UPSTREAM CG5718 INTRON CG44837	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
3R	10162768	3R_10162768_DEL [dm3] 3R_14337046_DEL [dm6]	TAAA	T	3.907e^-5	0.871	INTRON NK7.1	TF binding site mE1_TFBS_kn
3L	18730812	3L_18730812_SNP [dm3] 3L_18737712_SNP [dm6]	T	G	3.975e^-5	0.871	INTERGENIC
3R	27401973	3R_27401973_DEL [dm3] 3R_31576251_DEL [dm6]	TCCT	T	4.043e^-5	0.871	UTR_3_PRIME pygo DOWNSTREAM gammaCOP
3L	2465644	3L_2465644_SNP [dm3] 3L_2465644_SNP [dm6]	G	T	4.062e^-5	0.871	UTR_3_PRIME CG45186 DOWNSTREAM CG45186 INTRON CG45186
3R	10187548	3R_10187548_SNP [dm3] 3R_14361826_SNP [dm6]	G	T	4.126e^-5	0.871	UPSTREAM CG31320 INTRON NK7.1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	12019622	3R_12019622_SNP [dm3] 3R_16193900_SNP [dm6]	C	T	4.207e^-5	0.871	UPSTREAM sra INTRON sra
2R	9631828	2R_9631828_SNP [dm3] 2R_13744323_SNP [dm6]	G	A	4.220e^-5	0.871	INTRON fas
3R	6097864	3R_6097864_SNP [dm3] 3R_10272142_SNP [dm6]	A	G	4.252e^-5	0.871	INTRON CG43143
3R	9320113	3R_9320113_INS [dm3] 3R_13494391_INS [dm6]	T	TATTATA	4.394e^-5	0.871	INTERGENIC
3L	2471144	3L_2471144_SNP [dm3] 3L_2471144_SNP [dm6]	C	T	4.406e^-5	0.871	INTRON CG45186	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	9133338	3R_9133338_SNP [dm3] 3R_13307616_SNP [dm6]	A	G	4.412e^-5	0.871	INTRON CG32473
3R	25784282	3R_25784282_SNP [dm3] 3R_29958560_SNP [dm6]	T	G	4.424e^-5	0.871	INTRON TkR99D
2R	1072326	2R_1072326_INS [dm3] 2R_5184821_INS [dm6]	T	TT	4.460e^-5	0.871	INTRON Nipped-A
3R	26674736	3R_26674736_SNP [dm3] 3R_30849014_SNP [dm6]	A	C	4.527e^-5	0.871	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
2R	9631837	2R_9631837_DEL [dm3] 2R_13744332_DEL [dm6]	CCGC	C	4.536e^-5	0.871	INTRON fas
2L	2823295	2L_2823295_DEL [dm3] 2L_2823295_DEL [dm6]	TCTCT	T	4.664e^-5	0.871	DOWNSTREAM CG3123 INTRON Duox
3L	6748691	3L_6748691_SNP [dm3] 3L_6755591_SNP [dm6]	T	A	4.820e^-5	0.871	SYNONYMOUS_CODING CG10103	TF binding site mE1_TFBS_cad
2R	13133893	2R_13133893_SNP [dm3] 2R_17246388_SNP [dm6]	T	G	4.855e^-5	0.871	UPSTREAM CG18469 DOWNSTREAM CG12699 INTRON mbl
X	921614	X_921614_DEL [dm3] X_1027581_DEL [dm6]	CTC	C	5.109e^-5	0.871	UPSTREAM CG32814 & 1 other DOWNSTREAM CDC45L INTRON su_w[a]_ & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2L	14251897	2L_14251897_SNP [dm3] 2L_14251897_SNP [dm6]	G	A	5.165e^-5	0.871	INTERGENIC	TF binding site mE1_TFBS_bab1
3R	10974645	3R_10974645_DEL [dm3] 3R_15148923_DEL [dm6]	GAAG	G	5.168e^-5	0.871	INTERGENIC
3L	1666702	3L_1666702_DEL [dm3] 3L_1666702_DEL [dm6]	AGGTAGCTCA	A	5.212e^-5	0.871	UPSTREAM snoRNA:Me28S-A2634c DOWNSTREAM snoRNA:Me28S-A2634a & 2 others INTRON Uhg7 EXON snoRNA:Me28S-A2634b	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_zfh1
3R	8606136	3R_8606136_SNP [dm3] 3R_12780414_SNP [dm6]	T	G	5.260e^-5	0.871	INTRON beat-Vc
2L	6187063	2L_6187063_SNP [dm3] 2L_6187063_SNP [dm6]	T	C	5.294e^-5	0.871	INTRON CG34380	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	19387091	2R_19387091_SNP [dm3] 2R_23499568_SNP [dm6]	A	G	5.368e^-5	0.871	UPSTREAM CG13558 INTERGENIC	TF binding site BDTNP1_TFBS_sna
2R	14428846	2R_14428846_SNP [dm3] 2R_18541341_SNP [dm6]	G	A	5.424e^-5	0.871	INTRON Rgk2
2L	2823404	2L_2823404_DEL [dm3] 2L_2823404_DEL [dm6]	TGCTT	T	5.431e^-5	0.871	DOWNSTREAM CG3123 INTRON Duox
3R	25890739	3R_25890739_SNP [dm3] 3R_30065017_SNP [dm6]	C	A	5.486e^-5	0.871	INTRON sima	TF binding site BDTNP1_TFBS_twi
3R	9320110	3R_9320110_SNP [dm3] 3R_13494388_SNP [dm6]	G	A	5.502e^-5	0.871	INTERGENIC
3L	2471121	3L_2471121_SNP [dm3] 3L_2471121_SNP [dm6]	A	T	5.503e^-5	0.871	INTRON CG45186	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
X	918937	X_918937_SNP [dm3] X_1024904_SNP [dm6]	C	T	5.503e^-5	0.871	INTRON su_w[a]_ & 2 others	transposable element FlyBase
3L	8850557	3L_8850557_SNP [dm3] 3L_8857457_SNP [dm6]	T	C	5.532e^-5	0.871	INTRON dally
3R	20921929	3R_20921929_SNP [dm3] 3R_25096207_SNP [dm6]	T	C	5.613e^-5	0.871	DOWNSTREAM fd96Cb INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	18912293	2L_18912293_SNP [dm3] 2L_18912293_SNP [dm6]	C	T	5.632e^-5	0.871	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	5920643	X_5920643_SNP [dm3] X_6026610_SNP [dm6]	T	C	5.648e^-5	0.871	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	6090343	3R_6090343_SNP [dm3] 3R_10264621_SNP [dm6]	C	G	5.686e^-5	0.871	UTR_5_PRIME CG43143 DOWNSTREAM pont	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	10355035	2L_10355035_SNP [dm3] 2L_10355035_SNP [dm6]	A	G	5.695e^-5	0.871	INTRON CG5367
3L	14950276	3L_14950276_SNP [dm3] 3L_14957176_SNP [dm6]	G	A	5.716e^-5	0.871	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	10947030	3L_10947030_SNP [dm3] 3L_10953930_SNP [dm6]	T	C	5.740e^-5	0.871	INTERGENIC
3L	4083717	3L_4083717_SNP [dm3] 3L_4083717_SNP [dm6]	C	T	5.757e^-5	0.871	INTRON Gad1
3R	6079522	3R_6079522_SNP [dm3] 3R_10253800_SNP [dm6]	T	C	5.808e^-5	0.871	SYNONYMOUS_CODING CG3999	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens

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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=2.410e^-8)
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	4.625e-07

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.9827	0.0828

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1805 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

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	8521633	2L_8521633_SNP [dm3] 2L_8521633_SNP [dm6]	G	A	1.068e^-7	0.2	UTR_3_PRIME CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	23439912	3L_23439912_SNP [dm3] 3L_23446812_SNP [dm6]	T	A	5.971e^-7	0.494	INTERGENIC
2R	1081533	2R_1081533_DEL [dm3] 2R_5194028_DEL [dm6]	GT	G	7.901e^-7	0.494	INTRON Nipped-A	transposable element FlyBase
2L	13726505	2L_13726505_SNP [dm3] 2L_13726505_SNP [dm6]	G	T	1.574e^-6	0.542	INTERGENIC
2L	13726506	2L_13726506_SNP [dm3] 2L_13726506_SNP [dm6]	G	T	1.617e^-6	0.542	INTERGENIC
2L	5964672	2L_5964672_SNP [dm3] 2L_5964672_SNP [dm6]	G	A	1.733e^-6	0.542	UPSTREAM psd DOWNSTREAM CG13992 INTRON psd
3R	12799800	3R_12799800_SNP [dm3] 3R_16974078_SNP [dm6]	G	T	2.216e^-6	0.594	INTERGENIC	TF binding site BDTNP1_TFBS_slp1
2L	8520157	2L_8520157_SNP [dm3] 2L_8520157_SNP [dm6]	C	A	2.959e^-6	0.668	NON_SYNONYMOUS_CODING CG13091 DOWNSTREAM CG13090	TF binding site mE1_TFBS_chinmo
2L	5964676	2L_5964676_SNP [dm3] 2L_5964676_SNP [dm6]	A	G	3.628e^-6	0.668	UPSTREAM psd DOWNSTREAM CG13992 INTRON psd
2L	10345596	2L_10345596_SNP [dm3] 2L_10345596_SNP [dm6]	T	C	4.039e^-6	0.668	INTRON CG5022
3R	12799780	3R_12799780_SNP [dm3] 3R_16974058_SNP [dm6]	T	C	5.275e^-6	0.668	INTERGENIC	TF binding site BDTNP1_TFBS_slp1
3R	12799894	3R_12799894_SNP [dm3] 3R_16974172_SNP [dm6]	T	A	5.547e^-6	0.668	INTERGENIC	TF binding site BDTNP1_TFBS_slp1
3R	15907840	3R_15907840_SNP [dm3] 3R_20082118_SNP [dm6]	G	A	5.707e^-6	0.668	SYNONYMOUS_CODING Rh3	TF binding site mE1_TFBS_cad
3R	12799763	3R_12799763_INS [dm3] 3R_16974041_INS [dm6]	C	TCTTAAACTATGAGTG...	5.713e^-6	0.668	INTERGENIC
3R	12799805	3R_12799805_SNP [dm3] 3R_16974083_SNP [dm6]	T	C	5.982e^-6	0.668	INTERGENIC	TF binding site BDTNP1_TFBS_slp1
2L	313440	2L_313440_SNP [dm3] 2L_313440_SNP [dm6]	A	G	6.085e^-6	0.668	INTRON Plc21C
2L	10530516	2L_10530516_SNP [dm3] 2L_10530516_SNP [dm6]	T	C	6.578e^-6	0.668	SYNONYMOUS_CODING Lip4
3L	5460183	3L_5460183_SNP [dm3] 3L_5467083_SNP [dm6]	G	A	6.649e^-6	0.668	INTERGENIC
2R	1081532	2R_1081532_SNP [dm3] 2R_5194027_SNP [dm6]	T	A	6.766e^-6	0.668	INTRON Nipped-A	transposable element FlyBase
X	10933155	X_10933155_SNP [dm3] X_11039122_SNP [dm6]	G	C	8.321e^-6	0.734	INTRON CG42339	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
X	14846282	X_14846282_DEL [dm3] X_14952249_DEL [dm6]	ATATGTA	A	8.648e^-6	0.734	UPSTREAM pdgy DOWNSTREAM CR44831 INTRON pdgy	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	2457129	3R_2457129_SNP [dm3] 3R_6631407_SNP [dm6]	A	C	8.653e^-6	0.734	DOWNSTREAM sunz INTERGENIC
3R	19261728	3R_19261728_SNP [dm3] 3R_23436006_SNP [dm6]	G	A	9.351e^-6	0.734	INTRON CG4374
2L	4422778	2L_4422778_SNP [dm3] 2L_4422778_SNP [dm6]	A	G	9.536e^-6	0.734	INTRON CG15431
3R	19261520	3R_19261520_SNP [dm3] 3R_23435798_SNP [dm6]	A	T	9.781e^-6	0.734	INTRON CG4374
3R	14140329	3R_14140329_SNP [dm3] 3R_18314607_SNP [dm6]	G	C	1.020e^-5	0.736	UPSTREAM PKD INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	8512026	2L_8512026_SNP [dm3] 2L_8512026_SNP [dm6]	G	A	1.192e^-5	0.754	UPSTREAM CG13096 DOWNSTREAM CG13097 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA
3R	12799714	3R_12799714_SNP [dm3] 3R_16973992_SNP [dm6]	A	T	1.209e^-5	0.754	INTERGENIC
2L	4813253	2L_4813253_SNP [dm3] 2L_4813253_SNP [dm6]	A	C	1.248e^-5	0.754	UTR_5_PRIME CG15629
3R	2457128	3R_2457128_SNP [dm3] 3R_6631406_SNP [dm6]	C	G	1.254e^-5	0.754	DOWNSTREAM sunz INTERGENIC
2L	8521314	2L_8521314_SNP [dm3] 2L_8521314_SNP [dm6]	G	C	1.262e^-5	0.754	NON_SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
3R	23884709	3R_23884709_SNP [dm3] 3R_28058987_SNP [dm6]	G	A	1.332e^-5	0.754	INTRON CG34362
2R	14571614	2R_14571614_SNP [dm3] 2R_18684109_SNP [dm6]	A	G	1.372e^-5	0.754	UTR_5_PRIME CG44435 & 1 other DOWNSTREAM CG44433
2L	9125501	2L_9125501_SNP [dm3] 2L_9125501_SNP [dm6]	T	C	1.411e^-5	0.754	UPSTREAM CG32982 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_Kr
3R	23886018	3R_23886018_SNP [dm3] 3R_28060296_SNP [dm6]	C	T	1.443e^-5	0.754	INTRON CG34362
3R	23886156	3R_23886156_INS [dm3] 3R_28060434_INS [dm6]	T	TAT	1.450e^-5	0.754	INTRON CG34362
2L	13722023	2L_13722023_SNP [dm3] 2L_13722023_SNP [dm6]	T	C	1.488e^-5	0.754	DOWNSTREAM CG9014 INTERGENIC
2R	12253096	2R_12253096_SNP [dm3] 2R_16365591_SNP [dm6]	T	A	1.559e^-5	0.766	UTR_5_PRIME CG15711	TF binding site BDTNP1_TFBS_twi
2R	16439653	2R_16439653_SNP [dm3] 2R_20552148_SNP [dm6]	C	G	1.592e^-5	0.766	UPSTREAM CG13430 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Ubx
3L	18689778	3L_18689778_SNP [dm3] 3L_18696678_SNP [dm6]	C	T	1.642e^-5	0.77	UTR_3_PRIME Dic4 DOWNSTREAM Dic4
3R	15909618	3R_15909618_SNP [dm3] 3R_20083896_SNP [dm6]	T	C	1.688e^-5	0.772	INTERGENIC
3R	23884594	3R_23884594_SNP [dm3] 3R_28058872_SNP [dm6]	G	A	1.775e^-5	0.775	INTRON CG34362
3L	9137472	3L_9137472_SNP [dm3] 3L_9144372_SNP [dm6]	A	G	1.809e^-5	0.775	UTR_3_PRIME nwk UPSTREAM mir-4940 INTRON nwk	TF binding site mE1_TFBS_cad
2L	4639880	2L_4639880_SNP [dm3] 2L_4639880_SNP [dm6]	G	T	1.817e^-5	0.775	INTERGENIC
3R	12799734	3R_12799734_SNP [dm3] 3R_16974012_SNP [dm6]	A	T	1.882e^-5	0.785	INTERGENIC
3R	12799715	3R_12799715_SNP [dm3] 3R_16973993_SNP [dm6]	C	G	1.989e^-5	0.804	INTERGENIC
2L	20134738	2L_20134738_SNP [dm3] 2L_20134738_SNP [dm6]	A	G	2.057e^-5	0.804	INTRON CG10651
2L	1531313	2L_1531313_SNP [dm3] 2L_1531313_SNP [dm6]	G	A	2.132e^-5	0.804	INTERGENIC
3L	14524363	3L_14524363_SNP [dm3] 3L_14531263_SNP [dm6]	T	A	2.183e^-5	0.804	INTRON bbg
2L	8527621	2L_8527621_SNP [dm3] 2L_8527621_SNP [dm6]	T	C	2.241e^-5	0.804	SYNONYMOUS_CODING lmgB UTR_3_PRIME lmgA DOWNSTREAM lmgA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9512213	2R_9512213_SNP [dm3] 2R_13624708_SNP [dm6]	T	G	2.255e^-5	0.804	INTRON fas
2L	8504960	2L_8504960_SNP [dm3] 2L_8504960_SNP [dm6]	G	A	2.267e^-5	0.804	INTRON Dh31
2L	1531597	2L_1531597_SNP [dm3] 2L_1531597_SNP [dm6]	G	C	2.287e^-5	0.804	INTERGENIC
2L	313403	2L_313403_SNP [dm3] 2L_313403_SNP [dm6]	A	T	2.367e^-5	0.804	INTRON Plc21C
2L	10345624	2L_10345624_SNP [dm3] 2L_10345624_SNP [dm6]	G	T	2.462e^-5	0.804	INTRON CG5022
X	16051095	X_16051095_SNP [dm3] X_16157062_SNP [dm6]	C	G	2.481e^-5	0.804	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	15957612	3L_15957612_SNP [dm3] 3L_15964512_SNP [dm6]	G	T	2.485e^-5	0.804	SYNONYMOUS_CODING l_3_72Ab	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	13722385	2L_13722385_SNP [dm3] 2L_13722385_SNP [dm6]	T	G	2.515e^-5	0.804	UTR_3_PRIME CG9014
3R	11392803	3R_11392803_SNP [dm3] 3R_15567081_SNP [dm6]	G	C	2.528e^-5	0.804	INTERGENIC
2R	17111583	2R_17111583_SNP [dm3] 2R_21224078_SNP [dm6]	A	G	2.707e^-5	0.842	UPSTREAM ASPP INTRON ASPP
2L	8513770	2L_8513770_SNP [dm3] 2L_8513770_SNP [dm6]	G	A	2.860e^-5	0.842	SYNONYMOUS_CODING CG13097	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8513779	2L_8513779_SNP [dm3] 2L_8513779_SNP [dm6]	T	C	2.860e^-5	0.842	SYNONYMOUS_CODING CG13097	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	1017410	2R_1017410_SNP [dm3] 2R_5129905_SNP [dm6]	C	T	2.906e^-5	0.842	DOWNSTREAM CR43256 INTERGENIC
2R	9174432	2R_9174432_SNP [dm3] 2R_13286927_SNP [dm6]	T	C	2.915e^-5	0.842	INTRON Dh31-R
2L	8504943	2L_8504943_SNP [dm3] 2L_8504943_SNP [dm6]	T	C	2.917e^-5	0.842	INTRON Dh31
3L	19024253	3L_19024253_SNP [dm3] 3L_19031153_SNP [dm6]	T	A	3.037e^-5	0.863	INTRON nkd	TF binding site BDTNP1_TFBS_dl
2L	13050703	2L_13050703_SNP [dm3] 2L_13050703_SNP [dm6]	A	G	3.200e^-5	0.896	INTRON CG9932
3R	1956520	3R_1956520_SNP [dm3] 3R_6130798_SNP [dm6]	T	C	3.268e^-5	0.896	INTERGENIC
2L	12443152	2L_12443152_SNP [dm3] 2L_12443152_SNP [dm6]	A	G	3.334e^-5	0.896	SYNONYMOUS_CODING Oatp33Ea
2R	18708363	2R_18708363_DEL [dm3] 2R_22820858_DEL [dm6]	TT	T	3.343e^-5	0.896	UPSTREAM CG42284 INTRON CG30271	TF binding site mE1_TFBS_chinmo
3R	6194218	3R_6194218_INS [dm3] 3R_10368496_INS [dm6]	C	CA	3.421e^-5	0.904	INTRON Rfx	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	23848442	3R_23848442_INS [dm3] 3R_28022720_INS [dm6]	A	AA	3.662e^-5	0.943	INTERGENIC
2R	16439648	2R_16439648_SNP [dm3] 2R_20552143_SNP [dm6]	T	G	3.708e^-5	0.943	UPSTREAM CG13430 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_Ubx
3L	20904406	3L_20904406_SNP [dm3] 3L_20911306_SNP [dm6]	G	T	3.729e^-5	0.943	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	15309937	3R_15309937_SNP [dm3] 3R_19484215_SNP [dm6]	A	G	3.803e^-5	0.943	SYNONYMOUS_CODING Dys INTRON Dys
2L	8512075	2L_8512075_SNP [dm3] 2L_8512075_SNP [dm6]	A	T	3.861e^-5	0.943	UPSTREAM CG13096 DOWNSTREAM CG13097 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA
2L	15052450	2L_15052450_SNP [dm3] 2L_15052450_SNP [dm6]	T	C	3.888e^-5	0.943	INTRON ck	regulatory region REDfly_CRMs
3R	19463224	3R_19463224_SNP [dm3] 3R_23637502_SNP [dm6]	C	T	3.939e^-5	0.943	INTRON CG31145
3R	11416141	3R_11416141_SNP [dm3] 3R_15590419_SNP [dm6]	G	A	3.972e^-5	0.943	INTERGENIC
2L	12443179	2L_12443179_SNP [dm3] 2L_12443179_SNP [dm6]	G	A	4.066e^-5	0.953	SYNONYMOUS_CODING Oatp33Ea
3L	23338341	3L_23338341_SNP [dm3] 3L_23345241_SNP [dm6]	G	T	4.120e^-5	0.953	INTRON CG32230	transposable element FlyBase
2L	10452602	2L_10452602_INS [dm3] 2L_10452602_INS [dm6]	AG	CTA	4.255e^-5	0.953	UPSTREAM ppk10 DOWNSTREAM CG5322 INTERGENIC
2L	10452608	2L_10452608_INS [dm3] 2L_10452608_INS [dm6]	C	TGGA	4.255e^-5	0.953	UPSTREAM ppk10 DOWNSTREAM CG5322 INTERGENIC
2R	11545940	2R_11545940_SNP [dm3] 2R_15658435_SNP [dm6]	G	T	4.318e^-5	0.953	INTRON fus	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
3R	15907897	3R_15907897_SNP [dm3] 3R_20082175_SNP [dm6]	G	C	4.402e^-5	0.953	SYNONYMOUS_CODING Rh3	TF binding site mE1_TFBS_cad
3L	9143795	3L_9143795_SNP [dm3] 3L_9150695_SNP [dm6]	A	T	4.406e^-5	0.953	UTR_3_PRIME Rdl
2R	2780137	2R_2780137_SNP [dm3] 2R_6892632_SNP [dm6]	G	C	4.420e^-5	0.953	INTRON CG30158
3R	12799709	3R_12799709_SNP [dm3] 3R_16973987_SNP [dm6]	T	G	4.479e^-5	0.955	INTERGENIC
2L	8521447	2L_8521447_SNP [dm3] 2L_8521447_SNP [dm6]	C	T	4.531e^-5	0.955	UPSTREAM Acer INTRON CG13091	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
X	14470614	X_14470614_SNP [dm3] X_14576581_SNP [dm6]	T	C	4.595e^-5	0.958	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	23476747	3L_23476747_SNP [dm3] 3L_23483647_SNP [dm6]	G	T	4.774e^-5	0.961	INTERGENIC	transposable element FlyBase
X	14855617	X_14855617_SNP [dm3] X_14961584_SNP [dm6]	A	G	4.787e^-5	0.961	INTRON eag	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_chinmo
3R	16814302	3R_16814302_SNP [dm3] 3R_20988580_SNP [dm6]	C	T	4.794e^-5	0.961	UPSTREAM CG43446 & 1 other INTRON Calx
2L	313446	2L_313446_SNP [dm3] 2L_313446_SNP [dm6]	A	G	4.817e^-5	0.961	INTRON Plc21C
2L	13429582	2L_13429582_SNP [dm3] 2L_13429582_SNP [dm6]	T	A	5.033e^-5	0.981	INTRON CG42784	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2R	18369048	2R_18369048_SNP [dm3] 2R_22481543_SNP [dm6]	G	A	5.153e^-5	0.981	INTRON CG4752	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	7378830	2R_7378830_INS [dm3] 2R_11491325_INS [dm6]	C	CGAC	5.224e^-5	0.981	INTRON inv
3L	23228187	3L_23228187_SNP [dm3] 3L_23235087_SNP [dm6]	A	T	5.235e^-5	0.981	INTRON nAChRalpha4
3R	11416152	3R_11416152_SNP [dm3] 3R_15590430_SNP [dm6]	T	A	5.368e^-5	0.981	INTERGENIC
3R	16649476	3R_16649476_SNP [dm3] 3R_20823754_SNP [dm6]	T	C	5.409e^-5	0.981	DOWNSTREAM snoRNA:Psi28S-2562 & 2 others INTRON CG17272	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Cuticul_2_Me_C27_C28 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