Variant report

Variant	rs12117683
Chromosome Location	chr1:226286522-226286523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226286017..226288107-chr1:226288751..226292148,3	K562	blood:
2	chr1:226285884..226288013-chr1:226296594..226298367,3	K562	blood:
3	chr1:226248606..226253173-chr1:226284657..226288071,4	MCF-7	breast:
4	chr1:226260420..226263013-chr1:226284243..226287339,3	K562	blood:
5	chr1:226249583..226251274-chr1:226286013..226287713,2	K562	blood:
6	chr1:226185027..226186849-chr1:226285151..226286763,2	K562	blood:
7	chr1:226277702..226280605-chr1:226284688..226287302,2	MCF-7	breast:
8	chr1:226280306..226283507-chr1:226285698..226289497,4	K562	blood:
9	chr1:226280924..226283749-chr1:226285307..226289660,6	K562	blood:
10	chr1:226286017..226288107-chr1:226288751..226291625,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10915932	0.84[AFR][1000 genomes]
rs10915933	0.81[ASN][1000 genomes]
rs10915934	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915936	0.81[EUR][1000 genomes]
rs11577282	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12026319	0.93[ASN][1000 genomes]
rs12117819	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12121071	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12131977	0.83[ASN][1000 genomes]
rs12144544	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1355391	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4271181	0.83[AFR][1000 genomes]
rs7515023	0.81[EUR][1000 genomes]
rs7543135	0.83[AFR][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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12117683	H3F3A	cis	Esophagus Mucosa	GTEx
rs12117683	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs12117683	H3F3A	cis	Muscle Skeletal	GTEx
rs12117683	H3F3A	cis	Artery Aorta	GTEx
rs12117683	H3F3A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226271800-226288000	Weak transcription	Right Atrium	heart
2	chr1:226271800-226288400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:226272000-226287800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:226272000-226288200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:226278800-226287600	Weak transcription	Brain Anterior Caudate	brain
6	chr1:226281200-226295000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:226284800-226286600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:226284800-226286600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:226284800-226288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:226285400-226287000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:226285400-226287200	Enhancers	K562	blood
12	chr1:226285600-226286600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr1:226285800-226286600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr1:226286000-226286600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:226286200-226286800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:226286200-226287000	Enhancers	HMEC	breast
17	chr1:226286200-226287200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:226286200-226287800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:226286200-226287800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:226286200-226287800	Weak transcription	HSMM	muscle
21	chr1:226286200-226287800	Weak transcription	NH-A	brain
22	chr1:226286200-226287800	Weak transcription	NHDF-Ad	bronchial
23	chr1:226286200-226287800	Enhancers	NHEK	skin
24	chr1:226286200-226288000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:226286200-226288000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:226286200-226288400	Weak transcription	Esophagus	oesophagus
27	chr1:226286200-226297200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links