Variant report

Variant	rs12239898
Chromosome Location	chr1:196568696-196568697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10754193	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128003	1.00[ASN][1000 genomes]
rs12128544	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130004	1.00[ASN][1000 genomes]
rs12133309	1.00[ASN][1000 genomes]
rs12133639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134548	0.83[AMR][1000 genomes]
rs12136798	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13375443	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13375567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335906	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314834	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515738	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625226	1.00[EUR][1000 genomes]
rs4658040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58257510	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663649	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680890	1.00[EUR][1000 genomes]
rs6691524	0.83[ASN][1000 genomes]
rs73069765	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523548	1.00[ASN][1000 genomes]
rs7533533	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540922	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547724	1.00[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	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196557800-196574200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:196558000-196574400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:196558400-196574200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:196558400-196575000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:196560600-196571200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:196564000-196575800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:196568200-196569400	Enhancers	Liver	Liver
8	chr1:196568400-196568800	Enhancers	Fetal Lung	lung
9	chr1:196568400-196569000	Enhancers	Cortex derived primary cultured neurospheres	brain

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