Variant report

Variant	rs13068223
Chromosome Location	chr3:156470955-156470956
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	chr3:156392442..156394339-chr3:156468772..156471259,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-3	chr3:156470852-156471241	ENSG00000240875

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11709829	0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.80[ASN][1000 genomes]
rs11917436	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12107178	0.89[ASN][1000 genomes]
rs12638253	0.84[JPT][hapmap]
rs13061457	0.83[CHB][hapmap]
rs13067180	0.88[AFR][1000 genomes]
rs13088978	0.84[JPT][hapmap]
rs13095806	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13322318	0.89[JPT][hapmap]
rs13322900	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1469536	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap]
rs1560414	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1995425	0.84[JPT][hapmap]
rs2054880	0.88[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2321290	0.84[JPT][hapmap]
rs2321292	0.84[JPT][hapmap]
rs237250	0.83[TSI][hapmap]
rs34111024	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs343994	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs344027	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs344035	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs345985	0.80[CHB][hapmap]
rs36126086	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851992	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs4098	0.89[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4680312	0.84[JPT][hapmap]
rs4680317	0.84[JPT][hapmap]
rs6784421	0.84[JPT][hapmap]
rs7623691	0.83[ASN][1000 genomes]
rs7637701	0.84[JPT][hapmap]
rs7638625	0.84[JPT][hapmap]
rs8792	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9818684	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9818780	0.84[ASN][1000 genomes]
rs9822953	0.91[AFR][1000 genomes]
rs9837038	0.84[JPT][hapmap]
rs9838430	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs9847187	0.84[JPT][hapmap]
rs9859058	0.81[ASN][1000 genomes]
rs9865905	0.84[JPT][hapmap]
rs9867621	0.82[JPT][hapmap]
rs9867857	0.86[ASN][1000 genomes]
rs9868587	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9871817	0.84[JPT][hapmap]
rs9876010	0.84[JPT][hapmap]
rs9878566	0.84[ASN][1000 genomes]
rs9878585	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Age-related hearing impairment (interaction)	24939585	GWAS catalog

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156466800-156471200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:156468000-156471000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:156469200-156471000	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr3:156469400-156471200	Enhancers	HMEC	breast
5	chr3:156469600-156471400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:156469800-156471200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:156470000-156471000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:156470000-156471000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:156470000-156471200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:156470200-156471800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:156470200-156471800	Enhancers	NHDF-Ad	bronchial
12	chr3:156470200-156477800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:156470400-156471200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:156470800-156471000	Enhancers	Fetal Kidney	kidney
15	chr3:156470800-156478000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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