Variant report

Variant	rs10202878
Chromosome Location	chr2:47578684-47578685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10185866	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10195858	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10197484	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12996444	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025438	0.90[EUR][1000 genomes]
rs28609437	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4550710	0.82[ASN][1000 genomes]
rs4614976	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7581007	0.87[EUR][1000 genomes]
rs7584256	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv524003	chr2:47543245-47590034	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv581756	chr2:47552706-47590930	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1009586	chr2:47552706-47621487	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10202878	MSH2	cis	lung	GTEx
rs10202878	MSH2	cis	Artery Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47573800-47578800	Weak transcription	Fetal Kidney	kidney
2	chr2:47574400-47578800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:47574400-47580600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:47574400-47584400	Weak transcription	Right Atrium	heart
5	chr2:47574800-47579000	Weak transcription	Fetal Stomach	stomach
6	chr2:47574800-47579200	Weak transcription	Pancreas	Pancrea
7	chr2:47574800-47580600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:47574800-47581200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:47574800-47584200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:47575000-47581200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:47575000-47581200	Weak transcription	Stomach Mucosa	stomach
12	chr2:47575000-47586600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:47578000-47579600	Enhancers	HepG2	liver
14	chr2:47578000-47579800	Enhancers	Fetal Intestine Large	intestine
15	chr2:47578000-47583200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:47578200-47589600	Enhancers	Fetal Intestine Small	intestine
17	chr2:47578400-47579400	Enhancers	Fetal Lung	lung
18	chr2:47578600-47579000	Flanking Active TSS	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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