Variant report

Variant	rs17123650
Chromosome Location	chr1:85694671-85694672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85694538..85697394-chr1:85706640..85709318,2	MCF-7	breast:
2	chr1:85665411..85671906-chr1:85683759..85698338,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10493762	0.83[JPT][hapmap]
rs11161556	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161574	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11161584	0.85[EUR][1000 genomes]
rs11577656	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065422	0.86[MEX][hapmap]
rs12563295	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122364	0.84[JPT][hapmap]
rs17590006	1.00[YRI][hapmap]
rs2054238	0.83[JPT][hapmap]
rs2252408	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2647396	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735587	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735591	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735592	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735593	0.81[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2735594	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36006436	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768226	1.00[YRI][hapmap]
rs4255398	0.81[EUR][1000 genomes]
rs4907139	0.81[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4949892	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949926	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60156243	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693365	0.88[EUR][1000 genomes]
rs709790	0.80[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs72722613	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72722616	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72722624	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72722631	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722641	0.99[ASN][1000 genomes]
rs72722643	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7366220	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7531640	0.97[GIH][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17123650	C1orf52	cis	cerebellum	SCAN
rs17123650	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85687000-85709600	Weak transcription	Aorta	Aorta
2	chr1:85689400-85696000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:85690800-85696000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:85691400-85696200	Weak transcription	Right Ventricle	heart
5	chr1:85691600-85694800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:85691600-85695200	Weak transcription	Pancreas	Pancrea
7	chr1:85691600-85695200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:85691600-85695600	Weak transcription	Left Ventricle	heart
9	chr1:85691600-85696000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:85691600-85696200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:85691600-85696400	Weak transcription	Right Atrium	heart
12	chr1:85691800-85697000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:85692000-85695200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:85692000-85695400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:85692000-85695600	Weak transcription	Gastric	stomach
16	chr1:85692000-85696000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:85692000-85697400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:85692200-85695400	Weak transcription	K562	blood
19	chr1:85692200-85697400	Weak transcription	NHEK	skin
20	chr1:85694200-85695200	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:85694200-85696400	Enhancers	Fetal Heart	heart
22	chr1:85694200-85696400	Enhancers	Fetal Lung	lung
23	chr1:85694600-85696600	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links