Variant report

Variant	rs12997453
Chromosome Location	chr2:182413259-182413260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10203974	0.91[LWK][hapmap]
rs10204136	0.91[LWK][hapmap]
rs1026403	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10490692	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1143674	0.84[EUR][1000 genomes]
rs11886182	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11890431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478032	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12690516	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13003064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034078	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1349197	0.93[LWK][hapmap]
rs1375491	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1551031	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17226490	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2887191	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4667309	0.96[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs4667316	0.84[LWK][hapmap]
rs6707704	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6714061	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6721763	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6748657	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562325	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7602504	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1014910	chr2:182375267-182544114	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv536065	chr2:182375267-182544114	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv869674	chr2:182409485-182468632	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182401400-182417600	Weak transcription	NHDF-Ad	bronchial
2	chr2:182402800-182414600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:182405600-182413800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:182405600-182414600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:182405600-182415200	Weak transcription	Dnd41	blood
6	chr2:182406000-182415400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:182406200-182414600	Weak transcription	Thymus	Thymus
8	chr2:182406200-182414600	Weak transcription	GM12878-XiMat	blood
9	chr2:182406400-182415000	Weak transcription	Primary T cells from cord blood	blood
10	chr2:182406800-182415400	Weak transcription	Primary B cells from cord blood	blood
11	chr2:182406800-182418200	Weak transcription	Fetal Thymus	thymus
12	chr2:182410800-182419200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:182411200-182416800	Weak transcription	HMEC	breast
14	chr2:182411200-182417000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:182411200-182417000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links