Variant report

Variant	rs6456993
Chromosome Location	chr6:29670536-29670537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29670114..29670993-chr6:29802276..29803394,5	K562	blood:
2	chr10:38965666..38966167-chr6:29670107..29670640,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1122947	0.89[EUR][1000 genomes]
rs1984840	0.89[EUR][1000 genomes]
rs2079898	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517913	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2517941	0.80[EUR][1000 genomes]
rs2517943	0.80[EUR][1000 genomes]
rs2523401	0.80[EUR][1000 genomes]
rs2535245	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2535246	0.89[EUR][1000 genomes]
rs2735063	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2743950	0.80[EUR][1000 genomes]
rs2747425	0.84[EUR][1000 genomes]
rs2747453	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747455	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs29231	0.83[EUR][1000 genomes]
rs29273	0.82[EUR][1000 genomes]
rs2982837	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3095287	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129041	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129074	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129087	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129090	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131879	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131881	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3131882	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6941117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs730858	0.80[EUR][1000 genomes]
rs7738159	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776296	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9257931	0.83[EUR][1000 genomes]
rs9258093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9258094	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258106	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9258110	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9258111	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9258114	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258126	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9258127	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9258131	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6456993	HLA-H	cis	multi-tissue	Pritchard
rs6456993	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs6456993	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29670000-29670800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:29670200-29670600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:29670200-29670600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:29670200-29670600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:29670200-29670800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:29670200-29670800	Enhancers	Liver	Liver
8	chr6:29670200-29671000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr6:29670200-29671000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr6:29670200-29671000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr6:29670200-29678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:29670400-29670600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:29670400-29670600	Bivalent Enhancer	Brain Hippocampus Middle	brain
14	chr6:29670400-29670800	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:29670400-29670800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:29670400-29670800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr6:29670400-29671000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:29670400-29671000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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