Variant report

Variant	rs10861185
Chromosome Location	chr12:104676946-104676947
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10778321	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10861187	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs10861190	0.81[ASN][1000 genomes]
rs10861193	0.88[ASN][1000 genomes]
rs10861195	0.88[ASN][1000 genomes]
rs10861196	0.88[ASN][1000 genomes]
rs10861197	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs10861198	0.88[ASN][1000 genomes]
rs10861199	0.85[CEU][hapmap];0.88[ASN][1000 genomes]
rs11111938	0.85[JPT][hapmap]
rs11111940	0.86[JPT][hapmap]
rs11111945	0.81[JPT][hapmap]
rs11111979	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111980	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111981	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111984	0.88[ASN][1000 genomes]
rs11111987	0.85[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111995	0.88[ASN][1000 genomes]
rs11111996	0.88[ASN][1000 genomes]
rs12811618	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17202060	0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4075411	0.86[ASN][1000 genomes]
rs4445711	0.86[JPT][hapmap]
rs4595619	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4601859	0.88[ASN][1000 genomes]
rs4964782	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs4964783	0.86[ASN][1000 genomes]
rs4964785	0.83[ASN][1000 genomes]
rs5018287	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs7132675	0.80[ASN][1000 genomes]
rs7294778	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs7297956	0.82[JPT][hapmap]
rs7298739	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7310815	0.81[JPT][hapmap]
rs7488680	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs7954970	0.84[JPT][hapmap]
rs7958262	0.86[JPT][hapmap]
rs7962942	0.81[LWK][hapmap];0.80[MKK][hapmap]
rs7977410	0.82[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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10861185	TCP11L2	cis	cerebellum	SCAN
rs10861185	EID3	cis	Adipose Subcutaneous	GTEx
rs10861185	TDG	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104667600-104679600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104670400-104679600	Weak transcription	Thymus	Thymus
3	chr12:104670600-104679600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:104670600-104679800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:104674400-104679800	Weak transcription	Small Intestine	intestine
6	chr12:104674600-104677200	Enhancers	Hela-S3	cervix
7	chr12:104674600-104677800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:104674600-104678000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:104674600-104679400	Weak transcription	HSMMtube	muscle
10	chr12:104674600-104679600	Weak transcription	Aorta	Aorta
11	chr12:104674600-104679600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:104674600-104679600	Weak transcription	HepG2	liver
13	chr12:104674600-104679600	Weak transcription	HSMM	muscle
14	chr12:104674800-104679600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:104675000-104679400	Weak transcription	Stomach Mucosa	stomach
16	chr12:104675000-104679600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:104676000-104679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:104676000-104679600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:104676200-104678000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:104676200-104679400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:104676200-104679400	Weak transcription	NH-A	brain
22	chr12:104676400-104677200	Enhancers	A549	lung
23	chr12:104676400-104678400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:104676400-104678400	Weak transcription	HUVEC	blood vessel
25	chr12:104676400-104678600	Weak transcription	HMEC	breast
26	chr12:104676400-104678600	Weak transcription	NHEK	skin
27	chr12:104676400-104679000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:104676400-104679400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:104676400-104679400	Weak transcription	NHDF-Ad	bronchial
30	chr12:104676400-104679800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:104676600-104678400	Weak transcription	NHLF	lung
32	chr12:104676600-104678800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:104676600-104679200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:104676600-104679200	Weak transcription	Osteobl	bone
35	chr12:104676800-104679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:104676800-104679600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links