Variant report

Variant	rs13031209
Chromosome Location	chr2:47733535-47733536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11675417	0.86[CHB][hapmap]
rs11677098	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11891189	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13009248	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17036614	0.85[ASN][1000 genomes]
rs17036639	0.97[ASN][1000 genomes]
rs2042649	0.88[ASN][1000 genomes]
rs3771283	0.85[ASN][1000 genomes]
rs6544993	0.97[ASN][1000 genomes]
rs6751501	0.84[CHB][hapmap]
rs7584256	0.83[CEU][hapmap]
rs7587143	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13031209	MSH2	cis	lung	GTEx
rs13031209	MSH2	cis	Artery Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47729800-47733800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:47730400-47735600	Weak transcription	HUVEC	blood vessel
3	chr2:47731800-47733600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:47732400-47734000	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:47732600-47735800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:47732600-47747800	Weak transcription	Primary T cells from cord blood	blood
7	chr2:47733200-47733600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:47733200-47734000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:47733400-47734000	Enhancers	Brain Anterior Caudate	brain
10	chr2:47733400-47734000	Enhancers	Brain Hippocampus Middle	brain
11	chr2:47733400-47734000	Enhancers	Brain Substantia Nigra	brain

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links