Variant report

Variant	rs7004273
Chromosome Location	chr8:54428066-54428067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP6V1H-1	chr8:54427731-54429514	XLOC_007085
2	lnc-RGS20-1	chr8:54427730-54428166	ENSG00000254204
3	lnc-ATP6V1H-1	chr8:54426635-54429514	NONHSAT126594

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10095702	0.89[ASN][1000 genomes]
rs10958370	0.96[ASN][1000 genomes]
rs10958371	0.92[CEU][hapmap]
rs10958372	0.86[CEU][hapmap]
rs11776806	0.89[CEU][hapmap]
rs11778924	0.85[CEU][hapmap]
rs12541575	0.86[CEU][hapmap]
rs1477956	0.86[ASN][1000 genomes]
rs1477957	0.89[ASN][1000 genomes]
rs17361507	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs1904072	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6473839	0.89[ASN][1000 genomes]
rs6473840	0.89[ASN][1000 genomes]
rs6473842	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7812717	0.89[ASN][1000 genomes]
rs7829521	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752674	chr8:54181147-54483747	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7004273	RP11-1081M5.1	cis	Artery Tibial	GTEx
rs7004273	RP11-1081M5.2	cis	Artery Tibial	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54411800-54433400	Weak transcription	Colon Smooth Muscle	Colon
2	chr8:54419200-54436200	Weak transcription	Pancreas	Pancrea
3	chr8:54421800-54434800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:54422800-54434800	Weak transcription	Esophagus	oesophagus
5	chr8:54424000-54428400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:54426400-54433000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr8:54426400-54434600	Weak transcription	Fetal Muscle Leg	muscle
8	chr8:54426600-54429000	Enhancers	HSMMtube	muscle
9	chr8:54426600-54429200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr8:54426600-54430000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr8:54426800-54428800	Genic enhancers	Left Ventricle	heart
12	chr8:54426800-54429400	Strong transcription	Aorta	Aorta
13	chr8:54427000-54428200	Strong transcription	Fetal Stomach	stomach
14	chr8:54427000-54429600	Strong transcription	Ovary	ovary
15	chr8:54427200-54433200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:54427200-54433400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr8:54427400-54428600	Weak transcription	Fetal Heart	heart
18	chr8:54427400-54428800	Enhancers	NH-A	brain
19	chr8:54427400-54433000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:54427400-54434600	Weak transcription	NHLF	lung
21	chr8:54427600-54428200	Weak transcription	Right Ventricle	heart
22	chr8:54427600-54428400	Enhancers	HSMM	muscle
23	chr8:54427600-54429800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr8:54427600-54433200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:54427600-54433400	Weak transcription	HMEC	breast
26	chr8:54427800-54428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:54427800-54428200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:54427800-54429200	Genic enhancers	Osteobl	bone
29	chr8:54427800-54436200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:54428000-54428200	Enhancers	Spleen	Spleen
31	chr8:54428000-54434400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links