Variant report

Variant	rs28609437
Chromosome Location	chr2:47605097-47605098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47598530..47600190-chr2:47604958..47607928,2	K562	blood:
2	chr2:47601008..47603575-chr2:47604857..47606633,2	K562	blood:
3	chr2:47559485..47574826-chr2:47594341..47605593,65	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119888	Chromatin interaction
ENSG00000234690	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10185866	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10195858	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10197484	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202878	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12996444	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025438	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4614976	0.85[ASN][1000 genomes]
rs6726691	0.80[EUR][1000 genomes]
rs7581007	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7584256	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28609437	MSH2	cis	lung	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47597200-47610600	Weak transcription	Right Atrium	heart
2	chr2:47597200-47615000	Weak transcription	Esophagus	oesophagus
3	chr2:47597200-47619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:47597400-47607000	Weak transcription	Gastric	stomach
5	chr2:47597400-47614800	Weak transcription	HMEC	breast
6	chr2:47597400-47617000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:47597400-47629400	Weak transcription	NHEK	skin
8	chr2:47597600-47615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:47598600-47607000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:47598600-47607000	Weak transcription	Pancreas	Pancrea
11	chr2:47598600-47607200	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:47598600-47613000	Weak transcription	Lung	lung
13	chr2:47599000-47606200	Weak transcription	Fetal Kidney	kidney
14	chr2:47599200-47608000	Weak transcription	Fetal Stomach	stomach
15	chr2:47600200-47617800	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:47600400-47616800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:47600600-47614000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:47600600-47617200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:47600800-47614000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:47601000-47610200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr2:47601000-47610600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr2:47601000-47614200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:47601200-47609400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:47601200-47614600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:47601200-47616800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:47601200-47629400	Weak transcription	Stomach Mucosa	stomach
27	chr2:47601400-47610400	Weak transcription	Fetal Lung	lung
28	chr2:47601600-47607000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:47601600-47607800	Strong transcription	HepG2	liver
30	chr2:47601800-47605800	Strong transcription	Fetal Intestine Small	intestine
31	chr2:47602000-47607200	Weak transcription	Fetal Brain Male	brain
32	chr2:47602600-47605600	Strong transcription	Fetal Intestine Large	intestine
33	chr2:47602600-47610200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:47602800-47605400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:47602800-47607400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:47603200-47619000	Weak transcription	K562	blood
37	chr2:47604200-47605200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:47604400-47605400	Strong transcription	Colonic Mucosa	Colon
39	chr2:47604400-47606000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr2:47604600-47606200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:47604800-47605800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:47604800-47617000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:47604800-47628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:47605000-47606200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:47605000-47606600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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