Variant report

Variant	rs12580759
Chromosome Location	chr12:11800568-11800569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:11800508..11802179-chr12:11860722..11862273,2	MCF-7	breast:
2	chr12:11800455..11804262-chr12:12036773..12041762,7	MCF-7	breast:
3	chr12:11786072..11788465-chr12:11800287..11802406,2	K562	blood:
4	chr12:11784813..11787611-chr12:11800177..11801948,2	MCF-7	breast:
5	chr12:11800032..11801851-chr12:11845652..11848182,2	MCF-7	breast:
6	chr12:11800154..11802196-chr12:11905804..11907326,2	MCF-7	breast:
7	chr12:11799547..11802655-chr12:12030358..12032726,3	MCF-7	breast:
8	chr12:11800191..11804184-chr12:12034563..12039946,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12809794	0.85[ASN][1000 genomes]
rs12820094	0.85[ASN][1000 genomes]
rs12825857	0.85[ASN][1000 genomes]
rs12826301	0.85[ASN][1000 genomes]
rs12829015	0.82[EUR][1000 genomes]
rs12829658	0.82[EUR][1000 genomes]
rs12830471	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831402	0.85[ASN][1000 genomes]
rs2541119	0.85[ASN][1000 genomes]
rs2724625	0.85[ASN][1000 genomes]
rs2724627	0.85[ASN][1000 genomes]
rs2724632	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34038917	0.85[ASN][1000 genomes]
rs34364159	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34744715	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34771084	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34809544	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34826165	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34845319	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35250129	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35534801	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35651671	0.85[ASN][1000 genomes]
rs35929278	0.85[ASN][1000 genomes]
rs36060832	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71455399	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455400	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71455401	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7957020	0.85[ASN][1000 genomes]
rs7963043	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12580759	ETV6	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11792600-11801000	Weak transcription	HMEC	breast
2	chr12:11797200-11801200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:11797400-11801200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:11797400-11801400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:11798800-11801400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:11799600-11800800	Weak transcription	Fetal Brain Male	brain
7	chr12:11799800-11801000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:11800200-11800800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:11800200-11801000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links