Variant report

Variant	rs12471428
Chromosome Location	chr2:179687519-179687520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179670606..179674111-chr2:179686470..179689601,3	K562	blood:

Variant related genes	Relation type
ENSG00000155657	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10190741	0.84[GIH][hapmap]
rs11693372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12464151	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464215	0.84[GIH][hapmap]
rs12465459	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12469367	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12992014	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13006510	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17362581	0.88[MEX][hapmap]
rs1844334	1.00[ASN][1000 genomes]
rs1994546	0.85[YRI][hapmap]
rs2366912	0.87[ASN][1000 genomes]
rs3769858	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709708	0.82[MEX][hapmap]
rs6715406	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715901	0.80[ASW][hapmap]
rs6729746	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733291	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561149	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591782	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7592323	0.87[ASN][1000 genomes]
rs7600330	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179659400-179698000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:179674400-179691000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:179683200-179689000	Weak transcription	Left Ventricle	heart
4	chr2:179685000-179688800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:179685000-179689400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:179685000-179689600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:179685000-179689600	Weak transcription	Osteobl	bone
8	chr2:179685000-179692600	Weak transcription	Right Ventricle	heart
9	chr2:179685000-179693800	Weak transcription	HSMM	muscle
10	chr2:179685000-179694000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:179685200-179692000	Weak transcription	Primary T cells from cord blood	blood
12	chr2:179685200-179692200	Weak transcription	Aorta	Aorta
13	chr2:179685200-179692600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:179685200-179694000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:179685200-179694000	Weak transcription	HSMMtube	muscle
16	chr2:179685200-179698800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:179685600-179698200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:179685800-179689400	Weak transcription	HUVEC	blood vessel
19	chr2:179685800-179693400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:179685800-179698000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links