Variant report

Variant	rs10475077
Chromosome Location	chr5:1643812-1643813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1559974..1562443-chr5:1642820..1645262,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10040389	0.98[ASN][1000 genomes]
rs10052477	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10061756	0.84[ASN][1000 genomes]
rs10062809	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10062957	0.98[ASN][1000 genomes]
rs10074018	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10474721	0.98[ASN][1000 genomes]
rs10475075	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10475076	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153695	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41408448	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55854954	0.94[ASN][1000 genomes]
rs58775025	0.91[ASN][1000 genomes]
rs72719219	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72719222	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312909	0.85[ASN][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	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS 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	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv880788	chr5:1629407-1671200	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv881328	chr5:1637461-1671200	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10475077	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs10475077	CTD-2012J19.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10475077	CTD-2012J19.1	cis	lung	GTEx
rs10475077	RP11-43F13.1	cis	Muscle Skeletal	GTEx
rs10475077	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs10475077	CTD-2012J19.1	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1634600-1645000	Weak transcription	Right Atrium	heart
2	chr5:1634600-1645200	Weak transcription	Gastric	stomach
3	chr5:1643400-1644400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr5:1643600-1644000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
5	chr5:1643600-1644000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr5:1643600-1644000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:1643600-1644200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr5:1643600-1644200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
9	chr5:1643600-1644200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:1643600-1644200	Bivalent Enhancer	Fetal Thymus	thymus
11	chr5:1643600-1644400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
12	chr5:1643600-1644400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr5:1643600-1644400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr5:1643600-1644400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr5:1643600-1645000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr5:1643600-1645000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
17	chr5:1643600-1645600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
18	chr5:1643800-1644000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:1643800-1644000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:1643800-1644000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:1643800-1644000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:1643800-1644000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:1643800-1644000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:1643800-1644000	Flanking Bivalent TSS/Enh	Hela-S3	cervix
25	chr5:1643800-1644000	Bivalent Enhancer	NHDF-Ad	bronchial
26	chr5:1643800-1644200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:1643800-1644400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
28	chr5:1643800-1644600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links