Variant report

Variant	rs3094727
Chromosome Location	chr6:29672529-29672530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1476572	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476573	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610584	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610585	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610586	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610587	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610590	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610592	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610593	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610594	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610595	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610745	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611356	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611357	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611358	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1611359	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1611360	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1611361	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1611362	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1611363	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611365	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611366	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611368	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611369	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611370	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611372	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611375	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611376	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611377	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611378	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1611379	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1627465	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1736913	0.82[ASN][1000 genomes]
rs1736919	0.86[ASN][1000 genomes]
rs1736930	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736931	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394659	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394660	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894114	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3094726	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116788	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3116789	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116790	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116791	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116792	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116793	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116794	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3116795	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3116796	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3116797	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3129052	0.87[ASN][1000 genomes]
rs3131863	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131869	0.87[ASN][1000 genomes]
rs4711196	0.85[ASN][1000 genomes]
rs7739360	0.85[ASN][1000 genomes]
rs7739388	0.85[ASN][1000 genomes]
rs7759272	0.85[ASN][1000 genomes]
rs9258156	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv519888	chr6:29668537-29673483	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3094727	HCG4	cis	multi-tissue	Pritchard
rs3094727	KIT	trans	multi-tissue	Pritchard
rs3094727	HLA-A	cis	multi-tissue	Pritchard
rs3094727	HLA-H	cis	multi-tissue	Pritchard
rs3094727	HLA-F	cis	multi-tissue	Pritchard
rs3094727	FLJ35429	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29670200-29678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:29670600-29673200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:29670800-29673200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:29670800-29673600	Weak transcription	Liver	Liver
6	chr6:29670800-29678200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:29671000-29673200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:29672200-29673200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:29672200-29673200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links