Variant report

Variant	rs12563295
Chromosome Location	chr1:85686317-85686318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85684618..85687077-chr1:85688979..85691367,2	MCF-7	breast:
2	chr1:85665362..85671529-chr1:85685487..85692910,10	MCF-7	breast:
3	chr1:85668441..85670596-chr1:85684602..85686321,2	K562	blood:
4	chr1:85665411..85671906-chr1:85683759..85698338,27	MCF-7	breast:
5	chr1:85680889..85683525-chr1:85684219..85686902,3	K562	blood:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11161556	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161574	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11161584	0.84[EUR][1000 genomes]
rs11577656	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11583836	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17123650	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252408	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2735593	0.88[EUR][1000 genomes]
rs2735594	0.88[EUR][1000 genomes]
rs36006436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243776	0.81[EUR][1000 genomes]
rs4255398	0.84[EUR][1000 genomes]
rs4907139	0.84[EUR][1000 genomes]
rs4949892	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949926	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60156243	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6663690	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6671589	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693365	0.86[EUR][1000 genomes]
rs709790	0.83[ASN][1000 genomes]
rs72722613	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72722616	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72722624	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722638	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722641	0.97[ASN][1000 genomes]
rs72722643	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7366220	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12563295	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85668000-85689000	Weak transcription	Gastric	stomach
2	chr1:85673800-85690400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:85681400-85686600	Weak transcription	Stomach Mucosa	stomach
4	chr1:85681400-85690400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:85684400-85688200	Enhancers	Rectal Smooth Muscle	rectum
6	chr1:85684600-85687000	Enhancers	Colon Smooth Muscle	Colon
7	chr1:85684600-85689200	Enhancers	Fetal Stomach	stomach
8	chr1:85685400-85686400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:85685400-85686400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:85685400-85686400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:85685400-85686600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:85685400-85686600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:85685400-85687600	Enhancers	Fetal Heart	heart
14	chr1:85685400-85690000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:85685600-85686800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:85685600-85688400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:85685600-85690400	Enhancers	Fetal Lung	lung
18	chr1:85685800-85686400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:85685800-85686400	Weak transcription	Esophagus	oesophagus
20	chr1:85685800-85690800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:85686000-85686400	Enhancers	K562	blood
22	chr1:85686200-85686400	Enhancers	Fetal Intestine Large	intestine
23	chr1:85686200-85687400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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