Variant report

Variant	rs56681764
Chromosome Location	chr6:100915587-100915588
allele	C/T
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	CTBP2	chr6:100914974-100915963	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr6:100915317-100916351	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:100912882-100916388	H1-neurons	neurons:	n/a	n/a
4	USF2	chr6:100915552-100915607	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:100912776-100916575	H1-neurons	neurons:	n/a	n/a
6	ELF1	chr6:100915280-100915718	GM12878	blood:	n/a	n/a
7	TCF12	chr6:100915475-100915719	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100908327..100910621-chr6:100914553..100916127,2	MCF-7	breast:
2	chr6:100887185..100889268-chr6:100914294..100916955,2	MCF-7	breast:

Variant related genes	Relation type
SIM1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12663321	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12663539	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17054156	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17060650	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17060652	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3756915	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3798485	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73496769	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73496776	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73496787	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7746426	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9373553	1.00[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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100911800-100916000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr6:100912200-100915800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:100913400-100915600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr6:100913800-100916000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr6:100914400-100915600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
6	chr6:100914400-100915600	Bivalent Enhancer	Esophagus	oesophagus
7	chr6:100914400-100915800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr6:100914400-100915800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr6:100914400-100915800	Bivalent Enhancer	Fetal Thymus	thymus
10	chr6:100914600-100915600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
11	chr6:100914600-100915800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:100914600-100916200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
13	chr6:100914800-100915600	Bivalent Enhancer	Fetal Intestine Small	intestine
14	chr6:100914800-100915600	Enhancers	Gastric	stomach
15	chr6:100914800-100916000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
16	chr6:100915000-100915600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:100915000-100918200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:100915200-100915800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:100915200-100916000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr6:100915200-100916000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr6:100915400-100915600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:100915400-100915600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr6:100915400-100915600	Flanking Bivalent TSS/Enh	Liver	Liver
24	chr6:100915400-100915600	Bivalent Enhancer	HUVEC	blood vessel
25	chr6:100915400-100915800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
26	chr6:100915400-100915800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links