Variant report

Variant	rs1896909
Chromosome Location	chr12:30469203-30469204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:30469118-30469261	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000257932	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10843690	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050794	0.80[EUR][1000 genomes]
rs11050808	0.94[EUR][1000 genomes]
rs11050823	0.98[EUR][1000 genomes]
rs11050826	0.99[EUR][1000 genomes]
rs11050828	0.98[EUR][1000 genomes]
rs11513492	0.98[EUR][1000 genomes]
rs11608277	0.98[EUR][1000 genomes]
rs11612317	0.98[EUR][1000 genomes]
rs11613370	0.98[EUR][1000 genomes]
rs11613642	0.96[EUR][1000 genomes]
rs11614392	0.96[EUR][1000 genomes]
rs12424369	0.82[EUR][1000 genomes]
rs12425538	0.91[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap]
rs12815231	0.96[EUR][1000 genomes]
rs12823889	0.95[EUR][1000 genomes]
rs12826074	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831890	0.88[CEU][hapmap];0.83[GIH][hapmap];0.98[TSI][hapmap]
rs1429628	0.82[EUR][1000 genomes]
rs1652182	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1731489	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2010880	0.96[EUR][1000 genomes]
rs2099145	0.82[ASN][1000 genomes]
rs34300913	0.96[EUR][1000 genomes]
rs35004835	0.80[EUR][1000 genomes]
rs354136	0.98[EUR][1000 genomes]
rs61920761	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6487894	0.82[EUR][1000 genomes]
rs6487895	0.80[EUR][1000 genomes]
rs6487896	0.82[EUR][1000 genomes]
rs6487897	0.87[CEU][hapmap]
rs725063	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs7295282	0.82[EUR][1000 genomes]
rs7296820	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7298770	0.82[EUR][1000 genomes]
rs7303893	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs7304070	0.92[CEU][hapmap];0.97[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs7313186	0.88[EUR][1000 genomes]
rs7314209	0.87[EUR][1000 genomes]
rs7955178	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7956322	0.82[ASN][1000 genomes]
rs7964943	0.98[EUR][1000 genomes]
rs7972984	0.83[EUR][1000 genomes]
rs7978437	0.98[EUR][1000 genomes]
rs891318	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832360	chr12:30393329-30555693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv517916	chr12:30454845-30485611	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1896909	HCK	trans	lymphoblastoid	seeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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