Variant report

Variant	rs12523269
Chromosome Location	chr5:119867065-119867066
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	RAD21	chr5:119867032-119867260	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr5:119866983-119867095	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PRR16	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1154767	1.00[JPT][hapmap]
rs1404299	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404300	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17146710	1.00[CHB][hapmap]
rs1902147	1.00[CHB][hapmap]
rs2601211	1.00[CHB][hapmap]
rs2604163	1.00[CHB][hapmap]
rs41357149	1.00[CHB][hapmap]
rs4895161	1.00[JPT][hapmap]
rs56124912	0.83[AFR][1000 genomes]
rs6595236	1.00[CHB][hapmap]
rs6862090	1.00[JPT][hapmap]
rs7733602	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv462427	chr5:119838923-119928674	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599601	chr5:119838923-119928674	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119839800-119879800	Weak transcription	Psoas Muscle	Psoas
2	chr5:119854000-119868800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:119864400-119867200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:119864600-119871400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:119864600-119874200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:119864600-119874400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:119865400-119868600	Weak transcription	Osteobl	bone
8	chr5:119865400-119869600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:119865800-119874000	Weak transcription	HSMM	muscle
10	chr5:119866200-119867400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr5:119866400-119867200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr5:119866400-119867200	Enhancers	HSMMtube	muscle
13	chr5:119866800-119867400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:119867000-119867200	Flanking Bivalent TSS/Enh	Gastric	stomach
15	chr5:119867000-119867200	Enhancers	Left Ventricle	heart
16	chr5:119867000-119867400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr5:119867000-119867400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr5:119867000-119867400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr5:119867000-119867400	Enhancers	K562	blood
20	chr5:119867000-119867400	Enhancers	NHDF-Ad	bronchial
21	chr5:119867000-119869000	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links