Variant report

Variant	rs13009248
Chromosome Location	chr2:47736061-47736062
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11675417	0.86[CHB][hapmap]
rs11677098	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11891189	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12619323	0.84[ASN][1000 genomes]
rs13031209	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17036614	0.83[ASN][1000 genomes]
rs17036639	0.92[ASN][1000 genomes]
rs2042649	0.84[ASN][1000 genomes]
rs3771283	0.81[ASN][1000 genomes]
rs6544993	0.92[ASN][1000 genomes]
rs6751501	0.85[CHB][hapmap]
rs7587143	0.88[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13009248	MSH2	cis	lung	GTEx
rs13009248	MSH2	cis	Adipose Subcutaneous	GTEx
rs13009248	MSH2	cis	Artery Tibial	GTEx
rs13009248	MSH2	cis	Esophagus Muscularis	GTEx
rs13009248	MSH2	cis	Nerve Tibial	GTEx
rs13009248	MSH2	cis	Artery Aorta	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47732600-47747800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:47733600-47736800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:47733600-47739200	Weak transcription	Right Atrium	heart
4	chr2:47734000-47736600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:47734000-47740800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:47734000-47741000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:47734000-47741400	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:47734000-47747000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:47734000-47747600	Weak transcription	Brain Substantia Nigra	brain
10	chr2:47734800-47738200	Enhancers	Fetal Brain Male	brain
11	chr2:47735400-47737400	Enhancers	Dnd41	blood
12	chr2:47735400-47738400	Enhancers	Fetal Brain Female	brain
13	chr2:47735600-47737200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr2:47735600-47737200	Enhancers	HUVEC	blood vessel
15	chr2:47735800-47737200	Enhancers	Fetal Thymus	thymus
16	chr2:47736000-47736600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:47736000-47737000	ZNF genes & repeats	GM12878-XiMat	blood

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

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