Variant report

Variant	rs6808036
Chromosome Location	chr3:49236439-49236440
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:49236362-49237257	ECC-1	luminal epithelium:	n/a	chr3:49236959-49236967 chr3:49236934-49236944 chr3:49236623-49236630 chr3:49236620-49236635 chr3:49236622-49236632
2	MAX	chr3:49236393-49237204	ECC-1	luminal epithelium:	n/a	chr3:49236959-49236967 chr3:49236934-49236944 chr3:49236623-49236630 chr3:49236620-49236635 chr3:49236622-49236632

Variant related genes	Relation type
CCDC36	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10154992	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130183	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs12637346	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13084037	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082923	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099526	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs4384984	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955414	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955417	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4955421	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs4955439	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs6446256	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778080	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809851	0.88[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7429661	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432077	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834003	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9867285	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6808036	WDR6	cis	Heart Left Ventricle	GTEx
rs6808036	PFKFB4	cis	Nerve Tibial	GTEx
rs6808036	WDR6	cis	Muscle Skeletal	GTEx
rs6808036	AMT	cis	Adipose Subcutaneous	GTEx
rs6808036	AMT	cis	lung	GTEx
rs6808036	AMT	cis	Artery Tibial	GTEx
rs6808036	NICN1-AS1	cis	Thyroid	GTEx
rs6808036	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6808036	NICN1	cis	Thyroid	GTEx
rs6808036	AMT	cis	Whole Blood	GTEx
rs6808036	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs6808036	WDR6	cis	Nerve Tibial	GTEx
rs6808036	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs6808036	AMT	cis	Muscle Skeletal	GTEx
rs6808036	AMT	cis	Esophagus Mucosa	GTEx
rs6808036	AMT	cis	Thyroid	GTEx
rs6808036	AMT	cis	Artery Aorta	GTEx
rs6808036	AMT	cis	Nerve Tibial	GTEx
rs6808036	ARIH2	cis	Thyroid	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49235800-49237600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:49236000-49237000	Bivalent Enhancer	Placenta	Placenta
3	chr3:49236000-49238400	Enhancers	Fetal Heart	heart
4	chr3:49236200-49236600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:49236200-49236600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:49236200-49236600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:49236200-49236600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:49236200-49236600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:49236200-49236800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr3:49236200-49236800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr3:49236200-49236800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:49236200-49236800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr3:49236200-49237000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr3:49236200-49237200	Enhancers	HMEC	breast
15	chr3:49236200-49237800	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr3:49236400-49236600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:49236400-49236600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
18	chr3:49236400-49236600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:49236400-49236600	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr3:49236400-49236600	Bivalent Enhancer	Fetal Thymus	thymus
21	chr3:49236400-49236600	Flanking Active TSS	Ovary	ovary
22	chr3:49236400-49236600	Flanking Active TSS	Spleen	Spleen
23	chr3:49236400-49236600	Enhancers	HSMM	muscle
24	chr3:49236400-49236600	Flanking Active TSS	NHDF-Ad	bronchial
25	chr3:49236400-49236600	Flanking Active TSS	NHLF	lung
26	chr3:49236400-49236800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:49236400-49236800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr3:49236400-49236800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:49236400-49236800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
30	chr3:49236400-49236800	Flanking Active TSS	Esophagus	oesophagus
31	chr3:49236400-49236800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
32	chr3:49236400-49236800	Flanking Active TSS	Left Ventricle	heart
33	chr3:49236400-49236800	Flanking Active TSS	Lung	lung
34	chr3:49236400-49236800	Flanking Active TSS	Right Atrium	heart
35	chr3:49236400-49236800	Flanking Active TSS	Right Ventricle	heart
36	chr3:49236400-49236800	Enhancers	HSMMtube	muscle
37	chr3:49236400-49236800	Flanking Active TSS	Osteobl	bone
38	chr3:49236400-49237000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:49236400-49237000	Enhancers	Pancreas	Pancrea
40	chr3:49236400-49237200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:49236400-49237400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr3:49236400-49237400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
43	chr3:49236400-49237400	Active TSS	Brain Anterior Caudate	brain
44	chr3:49236400-49237400	Active TSS	Brain Substantia Nigra	brain
45	chr3:49236400-49237400	Active TSS	Colon Smooth Muscle	Colon
46	chr3:49236400-49237400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr3:49236400-49237400	Bivalent/Poised TSS	Fetal Brain Female	brain
48	chr3:49236400-49237400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
49	chr3:49236400-49237400	Active TSS	Fetal Kidney	kidney
50	chr3:49236400-49237400	Active TSS	Rectal Mucosa Donor 31	rectum

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