Variant report

Variant	rs2066640
Chromosome Location	chr13:50769940-50769941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50769169..50772786-chr13:50775972..50780141,4	MCF-7	breast:
2	chr13:50769446..50774611-chr13:50774663..50778768,6	K562	blood:
3	chr13:50655124..50656827-chr13:50768354..50770224,2	K562	blood:

Variant related genes	Relation type
ENSG00000176124	Chromatin interaction
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1007852	0.84[JPT][hapmap]
rs1326127	0.82[AMR][1000 genomes]
rs1965800	0.80[JPT][hapmap]
rs2049286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2066629	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066632	0.84[JPT][hapmap]
rs2066639	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066654	0.94[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066660	0.82[AMR][1000 genomes]
rs2580187	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2580188	0.82[JPT][hapmap]
rs2580190	0.84[AMR][1000 genomes]
rs2703082	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2740516	0.80[JPT][hapmap]
rs2740521	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2740522	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2740523	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765763	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765767	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2812196	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv561631	chr13:50761619-50846748	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50760600-50789200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:50761200-50776400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:50763800-50770400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr13:50766600-50772000	Weak transcription	Hela-S3	cervix
5	chr13:50766800-50770600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:50767000-50782800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:50767000-50783000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr13:50767200-50777400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:50767600-50782800	Weak transcription	Gastric	stomach
10	chr13:50767800-50782800	Weak transcription	Colonic Mucosa	Colon
11	chr13:50768800-50771800	Weak transcription	K562	blood
12	chr13:50769000-50771600	Weak transcription	Fetal Heart	heart
13	chr13:50769600-50774400	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links