Variant report

Variant	rs1196882
Chromosome Location	chr12:105486447-105486448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105485255..105487201-chr12:105499969..105501573,2	K562	blood:
2	chr12:105484191..105488176-chr12:105493160..105495554,3	MCF-7	breast:
3	chr12:105351971..105353693-chr12:105484339..105486678,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257999	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000136052	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10778366	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861327	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10861328	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861329	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861330	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861331	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861332	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861333	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861335	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861336	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11112347	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112349	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112350	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112351	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11112352	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11112356	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11611105	0.89[CHB][hapmap]
rs11612252	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11613233	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11613261	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1196758	0.85[CEU][hapmap]
rs1196766	0.89[CEU][hapmap]
rs1196767	0.89[CEU][hapmap]
rs1196768	0.91[CEU][hapmap]
rs1196781	0.89[CEU][hapmap]
rs1196788	0.89[CEU][hapmap]
rs1196796	0.89[CEU][hapmap]
rs1196804	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs1196814	0.89[CEU][hapmap]
rs1196836	0.88[CEU][hapmap];0.88[YRI][hapmap]
rs1196838	0.86[CEU][hapmap];0.82[YRI][hapmap]
rs1196878	0.85[CEU][hapmap]
rs1196879	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196880	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1196886	0.98[ASN][1000 genomes]
rs1201657	0.89[CEU][hapmap]
rs12367626	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581638	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17242777	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1732377	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2246510	0.85[CEU][hapmap]
rs2264066	0.89[CEU][hapmap]
rs2374448	0.89[CEU][hapmap]
rs2374451	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2440693	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440708	0.88[CEU][hapmap]
rs2440717	0.88[CEU][hapmap]
rs4144467	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4144468	0.96[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56118650	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56188643	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56369757	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61938827	0.83[EUR][1000 genomes]
rs727888	0.89[CEU][hapmap]
rs7308195	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310488	0.89[CEU][hapmap]
rs7311691	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73179949	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7962686	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh 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	20 gene(s)	inside rSNPs	diseases
3	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105483200-105487000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:105484400-105486600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:105484800-105487000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:105485400-105486800	Enhancers	Brain Substantia Nigra	brain
5	chr12:105485400-105486800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:105485600-105486600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:105485800-105487000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:105485800-105487000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:105486000-105486600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:105486000-105486600	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr12:105486000-105486600	Active TSS	Duodenum Mucosa	Duodenum
12	chr12:105486000-105486600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
13	chr12:105486000-105486600	Active TSS	Pancreas	Pancrea
14	chr12:105486000-105486800	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr12:105486200-105486600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:105486200-105486600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:105486200-105486600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:105486200-105486600	Active TSS	Esophagus	oesophagus
19	chr12:105486200-105486800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:105486200-105486800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:105486200-105486800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:105486200-105486800	Flanking Active TSS	NHEK	skin
23	chr12:105486400-105486600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr12:105486400-105486600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
25	chr12:105486400-105486600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:105486400-105486600	Active TSS	Placenta	Placenta
27	chr12:105486400-105486800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:105486400-105486800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:105486400-105486800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:105486400-105486800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:105486400-105486800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr12:105486400-105486800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:105486400-105486800	Flanking Active TSS	HMEC	breast
34	chr12:105486400-105487000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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