Variant report

Variant	rs12310129
Chromosome Location	chr12:49751188-49751189
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49749944..49753062-chr12:49757524..49761259,4	K562	blood:
2	chr12:49743602..49746884-chr12:49748711..49752212,3	K562	blood:
3	chr12:49725555..49726058-chr12:49750586..49751591,3	K562	blood:
4	chr12:49750929..49751963-chr12:49907319..49908585,3	MCF-7	breast:
5	chr12:49750635..49751535-chr12:49951399..49952213,2	MCF-7	breast:
6	chr12:49690516..49692024-chr12:49750508..49752011,2	K562	blood:
7	chr12:49691633..49692545-chr12:49750700..49751496,2	MCF-7	breast:
8	chr12:49725096..49726573-chr12:49750546..49751554,11	MCF-7	breast:
9	chr12:49751120..49753975-chr12:49908043..49912245,4	K562	blood:
10	chr12:49681812..49682734-chr12:49750562..49751558,2	K562	blood:
11	chr12:49749539..49755045-chr12:49758003..49762481,13	MCF-7	breast:
12	chr12:49681807..49682815-chr12:49750578..49751528,4	MCF-7	breast:
13	chr12:49750854..49751500-chr12:49907554..49908179,2	MCF-7	breast:
14	chr12:49750309..49752657-chr12:49754226..49756226,3	MCF-7	breast:
15	chr12:49737855..49743235-chr12:49749199..49753144,5	K562	blood:
16	chr12:49750823..49752635-chr12:49950607..49952469,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPATS2-1	chr12:49750932-49751309	NONHSAT028104

No data

Variant related genes	Relation type
ENSG00000135406	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000178401	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10506284	1.00[JPT][hapmap]
rs10506285	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11168981	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11169016	1.00[JPT][hapmap]
rs11169058	1.00[JPT][hapmap]
rs11169059	1.00[JPT][hapmap]
rs11831313	1.00[ASN][1000 genomes]
rs11834161	1.00[JPT][hapmap]
rs11835071	0.94[ASN][1000 genomes]
rs12296440	1.00[JPT][hapmap]
rs12299777	0.81[ASN][1000 genomes]
rs12301632	1.00[JPT][hapmap]
rs12305716	1.00[JPT][hapmap]
rs12306118	1.00[JPT][hapmap]
rs12306866	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12309053	1.00[JPT][hapmap]
rs12315996	1.00[JPT][hapmap]
rs12317856	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12322561	1.00[JPT][hapmap]
rs17123696	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17123751	1.00[JPT][hapmap]
rs17197593	1.00[JPT][hapmap]
rs1874909	0.94[ASN][1000 genomes]
rs1874910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1874911	0.94[ASN][1000 genomes]
rs2270741	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2272478	1.00[JPT][hapmap]
rs60331259	1.00[ASN][1000 genomes]
rs60494978	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	1.00[JPT][hapmap]
rs6580709	1.00[JPT][hapmap]
rs6580716	1.00[JPT][hapmap]
rs7139061	1.00[JPT][hapmap]
rs7294648	1.00[JPT][hapmap]
rs7294973	1.00[JPT][hapmap]
rs7295162	1.00[JPT][hapmap]
rs7309997	1.00[JPT][hapmap]
rs7342365	1.00[JPT][hapmap]
rs74089059	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs74089062	0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7955245	1.00[ASN][1000 genomes]
rs7955541	1.00[JPT][hapmap]
rs7962951	1.00[JPT][hapmap]
rs7969099	1.00[JPT][hapmap]
rs7976165	1.00[JPT][hapmap]
rs9919740	1.00[JPT][hapmap]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49743400-49752200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:49743600-49752400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:49743600-49752400	Weak transcription	Stomach Mucosa	stomach
4	chr12:49743800-49752400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:49744800-49752400	Weak transcription	HepG2	liver
6	chr12:49745400-49752400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:49745800-49752200	Weak transcription	Fetal Intestine Large	intestine
8	chr12:49747400-49752400	Weak transcription	Liver	Liver
9	chr12:49747600-49752400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:49750600-49752200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:49750600-49753000	Enhancers	HSMM	muscle
12	chr12:49750800-49751200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:49750800-49752400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:49750800-49752400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:49750800-49752800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:49750800-49753000	Enhancers	NHDF-Ad	bronchial
17	chr12:49750800-49753800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links