Variant report

Variant	rs3759273
Chromosome Location	chr12:10458021-10458022
allele	A/C
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	STAT3	chr12:10458018-10458234	MCF10A-Er-Src	breast:	n/a	chr12:10458125-10458136

Variant related genes	Relation type
KLRD1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11053738	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11053739	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11053740	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611333	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs12829155	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1600130	0.89[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2270238	0.90[GIH][hapmap]
rs2302489	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2537752	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2537781	0.92[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2617146	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759270	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3759272	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809214	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3867486	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3912117	0.89[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3927994	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61242400	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7135494	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301715	0.82[EUR][1000 genomes]
rs7313418	0.82[CEU][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs7314888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316530	0.82[EUR][1000 genomes]
rs7964452	0.87[EUR][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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv605	chr12:10448638-10494208	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3759273	NOP2	cis	cerebellum	SCAN
rs3759273	KLRA1	cis	cerebellum	SCAN
rs3759273	ATN1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10453200-10461000	Weak transcription	Placenta	Placenta
2	chr12:10454800-10474400	Weak transcription	Left Ventricle	heart
3	chr12:10457600-10458200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:10457600-10458200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr12:10457600-10458200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr12:10457600-10458400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr12:10457800-10458400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr12:10458000-10458400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:10458000-10458400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:10458000-10464200	Active TSS	Primary T cells fromperipheralblood	blood

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