Variant report

Variant	rs4713069
Chromosome Location	chr6:27128307-27128308
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:27124141..27131442-chr6:27773840..27780959,15	K562	blood:
2	chr6:27127283..27131812-chr6:27144311..27148515,7	MCF-7	breast:
3	chr6:27127171..27129409-chr6:27778202..27780210,2	K562	blood:
4	chr6:27127689..27130005-chr6:27798100..27799751,2	MCF-7	breast:
5	chr6:27127869..27129685-chr6:27862673..27865192,2	K562	blood:
6	chr6:27128299..27130552-chr6:27519554..27521121,2	K562	blood:
7	chr6:27127808..27129505-chr6:27189088..27190771,2	K562	blood:
8	chr6:27128242..27130382-chr6:27772213..27774581,2	K562	blood:
9	chr6:27128038..27130307-chr6:27858390..27861349,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000217862	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1028308	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10456352	0.85[JPT][hapmap]
rs10946891	0.85[JPT][hapmap]
rs1102558	0.80[ASN][1000 genomes]
rs1102564	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1102565	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11756275	0.90[JPT][hapmap]
rs12527111	0.90[JPT][hapmap]
rs2022272	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2142685	0.90[JPT][hapmap]
rs2393915	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4583981	0.85[JPT][hapmap]
rs6456767	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs6456768	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6921388	0.95[JPT][hapmap]
rs6925226	0.81[ASN][1000 genomes]
rs6930508	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6937880	0.85[JPT][hapmap]
rs7744759	0.90[JPT][hapmap]
rs7747454	0.90[JPT][hapmap]
rs858964	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs858967	0.80[ASN][1000 genomes]
rs858968	0.80[ASN][1000 genomes]
rs858969	0.80[ASN][1000 genomes]
rs858970	0.80[ASN][1000 genomes]
rs858972	0.85[JPT][hapmap]
rs858974	0.83[ASN][1000 genomes]
rs858976	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs858977	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9295730	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9379958	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs9379960	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9393790	0.90[JPT][hapmap]
rs9393791	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9461335	0.81[ASN][1000 genomes]
rs994691	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]

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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4713069	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27125800-27128800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:27125800-27128800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:27125800-27129000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:27126000-27128600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:27126000-27129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:27126000-27135800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:27126200-27128400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:27126200-27128400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:27126200-27128600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:27126200-27128600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:27126200-27128600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:27126200-27128800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:27126200-27129200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:27126200-27129200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:27126200-27129200	Weak transcription	NHEK	skin
16	chr6:27126200-27129400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:27126200-27129400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:27126200-27131200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:27126200-27136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:27126400-27128600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:27126400-27128600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:27126400-27129200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:27126400-27129200	Weak transcription	GM12878-XiMat	blood
24	chr6:27126400-27129200	Weak transcription	Hela-S3	cervix
25	chr6:27126400-27129400	Weak transcription	A549	lung
26	chr6:27126400-27131400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:27127200-27129000	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links