Variant report

Variant	rs1980083
Chromosome Location	chr1:94207992-94207993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94207201..94209502-chr1:94212194..94214368,2	K562	blood:
2	chr1:94203575..94205213-chr1:94206735..94208348,2	K562	blood:
3	chr1:94206892..94209367-chr1:94213428..94215189,2	MCF-7	breast:
4	chr1:94075553..94077277-chr1:94206889..94209236,2	MCF-7	breast:
5	chr1:94145960..94147486-chr1:94206281..94208369,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10489602	0.82[CEU][hapmap]
rs10489604	0.81[CEU][hapmap]
rs10782966	0.81[EUR][1000 genomes]
rs10782967	0.81[EUR][1000 genomes]
rs11164974	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11164976	0.90[YRI][hapmap]
rs11800779	0.82[YRI][hapmap]
rs12140446	0.81[CEU][hapmap]
rs1884018	0.86[CEU][hapmap]
rs2235971	0.81[CEU][hapmap]
rs2747039	0.81[EUR][1000 genomes]
rs2747041	0.81[EUR][1000 genomes]
rs2747042	0.85[CHB][hapmap]
rs2747045	0.86[CEU][hapmap]
rs2818160	0.81[EUR][1000 genomes]
rs2818162	0.81[EUR][1000 genomes]
rs3747965	0.81[CEU][hapmap]
rs4075523	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4141737	0.81[CEU][hapmap]
rs4240955	0.81[EUR][1000 genomes]
rs4240956	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4314890	0.81[EUR][1000 genomes]
rs4520428	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs4847255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847256	0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847257	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6541395	0.82[YRI][hapmap]
rs6660210	0.85[CHB][hapmap]
rs6664719	0.81[CEU][hapmap]
rs6684389	0.84[YRI][hapmap]
rs7552293	0.85[CHB][hapmap]
rs8179391	0.81[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1980083	RP11-488P3.1	cis	Thyroid	GTEx
rs1980083	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs1980083	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs1980083	RP11-488P3.1	cis	lung	GTEx
rs1980083	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1980083	RP11-488P3.1	cis	Artery Tibial	GTEx
rs1980083	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs1980083	RP11-488P3.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94199400-94217400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94204000-94208200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:94205000-94209400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:94205400-94208000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:94205800-94209200	Enhancers	HepG2	liver
6	chr1:94206000-94210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:94206000-94212600	Weak transcription	HMEC	breast
8	chr1:94206200-94209400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:94206200-94209400	Weak transcription	NHEK	skin
10	chr1:94206200-94211600	Weak transcription	Spleen	Spleen
11	chr1:94206600-94209400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:94206800-94210000	Weak transcription	Left Ventricle	heart
13	chr1:94206800-94212400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:94206800-94212400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:94207000-94208600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:94207000-94210000	Weak transcription	Fetal Lung	lung
17	chr1:94207000-94211200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:94207600-94208000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr1:94207600-94208200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:94207800-94209000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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