Variant report

Variant	rs9851770
Chromosome Location	chr3:134160593-134160594
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	chr3:134091048..134093142-chr3:134160281..134163613,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114019	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11916983	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11917131	0.91[ASN][1000 genomes]
rs11917156	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11924801	0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12695612	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695613	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059980	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13066038	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13067502	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13067509	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13074369	0.91[ASN][1000 genomes]
rs13075432	0.89[ASN][1000 genomes]
rs13097818	0.86[CHB][hapmap]
rs1366067	0.81[AMR][1000 genomes]
rs1391695	0.80[AMR][1000 genomes]
rs2241557	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34102849	0.91[ASN][1000 genomes]
rs35088484	0.91[ASN][1000 genomes]
rs35394720	0.91[ASN][1000 genomes]
rs35922016	0.91[ASN][1000 genomes]
rs35944310	0.91[ASN][1000 genomes]
rs4312629	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4552325	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4596118	0.91[ASN][1000 genomes]
rs4605513	0.91[ASN][1000 genomes]
rs4607082	0.91[ASN][1000 genomes]
rs4974488	0.80[AMR][1000 genomes]
rs6771701	0.91[ASN][1000 genomes]
rs6791295	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796705	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7623580	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637740	0.86[CHB][hapmap]
rs7644093	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7644251	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7647128	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9789971	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9789972	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9809989	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9822766	0.91[ASN][1000 genomes]
rs9826589	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829477	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9829637	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9835166	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839295	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9848223	0.88[ASN][1000 genomes]
rs9857134	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv967068	chr3:134153022-134165125	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9851770	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs9851770	KY	cis	cerebellum	SCAN
rs9851770	ANAPC13	cis	Muscle Skeletal	GTEx
rs9851770	ANAPC13	cis	parietal	SCAN
rs9851770	ANAPC13	cis	Artery Tibial	GTEx
rs9851770	ANAPC13	cis	lung	GTEx
rs9851770	ANAPC13	cis	Thyroid	GTEx
rs9851770	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs9851770	ANAPC13	cis	cerebellum	SCAN
rs9851770	ANAPC13	cis	lesional skin	skin_eQTL
rs9851770	TXNDC6	cis	cerebellum	SCAN
rs9851770	ANAPC13	cis	Esophagus Muscularis	GTEx
rs9851770	ANAPC13	cis	Nerve Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134159200-134161200	Enhancers	Osteobl	bone
2	chr3:134159400-134161400	Enhancers	HMEC	breast
3	chr3:134159600-134160800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:134159800-134160600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:134159800-134160800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:134159800-134161000	Enhancers	NHEK	skin
7	chr3:134159800-134161200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134159800-134161600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:134160200-134161400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:134160400-134161200	Enhancers	NHDF-Ad	bronchial
11	chr3:134160400-134162400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:134160400-134164400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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