Variant report

Variant	rs12478848
Chromosome Location	chr2:178932959-178932960
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178925975..178933021-chr2:178933088..178941034,14	K562	blood:
2	chr2:178932912..178934541-chr2:178939711..178942332,2	K562	blood:
3	chr2:178929469..178931467-chr2:178932896..178934478,2	K562	blood:

Variant related genes	Relation type
ENSG00000128655	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1020010	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10211367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10930820	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12472886	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12473461	0.95[JPT][hapmap]
rs12477170	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12478277	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12618606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12621562	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12990719	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1527286	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1527287	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1527293	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1527294	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1527295	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1527296	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1534289	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1546813	0.94[JPT][hapmap]
rs1554776	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs17636610	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs17687590	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17687668	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1821629	0.93[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs1830209	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1836672	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1852496	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1852497	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1852499	0.81[ASN][1000 genomes]
rs1982131	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1991994	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2009303	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2043547	0.84[CEU][hapmap]
rs2060490	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2060491	0.81[ASN][1000 genomes]
rs2117738	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2117740	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4335982	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4567975	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4893844	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4893994	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4893995	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs62183413	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6433710	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6726809	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6750869	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6758442	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs744397	0.94[JPT][hapmap]
rs744398	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570423	0.94[JPT][hapmap]
rs934568	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9679090	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178929200-178934200	Weak transcription	Fetal Intestine Small	intestine
2	chr2:178931600-178937000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:178932000-178934200	Weak transcription	Pancreas	Pancrea
4	chr2:178932000-178936600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:178932800-178933200	Weak transcription	K562	blood
6	chr2:178932800-178934400	Weak transcription	HepG2	liver

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