Variant report

Variant	rs2130001
Chromosome Location	chr3:119859055-119859056
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	chr3:119813985..119815487-chr3:119857382..119859255,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10049256	0.87[EUR][1000 genomes]
rs10934512	0.87[EUR][1000 genomes]
rs10934514	0.83[EUR][1000 genomes]
rs10934515	0.87[EUR][1000 genomes]
rs10934516	0.87[EUR][1000 genomes]
rs10934517	0.87[EUR][1000 genomes]
rs11707711	0.87[EUR][1000 genomes]
rs12152218	0.86[EUR][1000 genomes]
rs1352458	0.87[EUR][1000 genomes]
rs1488761	0.87[EUR][1000 genomes]
rs1488762	0.87[EUR][1000 genomes]
rs1488764	0.87[EUR][1000 genomes]
rs1907681	0.87[EUR][1000 genomes]
rs2035671	0.87[EUR][1000 genomes]
rs2035672	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2035673	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2035674	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130000	0.87[EUR][1000 genomes]
rs2171598	0.87[EUR][1000 genomes]
rs2171599	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2319541	0.87[EUR][1000 genomes]
rs2319542	0.87[EUR][1000 genomes]
rs2319543	0.87[EUR][1000 genomes]
rs28398784	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2874022	0.87[EUR][1000 genomes]
rs2874023	0.87[EUR][1000 genomes]
rs3112282	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3112283	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs334549	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4488869	0.93[EUR][1000 genomes]
rs4676804	0.87[EUR][1000 genomes]
rs4676809	0.87[EUR][1000 genomes]
rs4676822	0.87[EUR][1000 genomes]
rs4676832	0.80[EUR][1000 genomes]
rs6438558	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6438559	0.93[EUR][1000 genomes]
rs6438561	0.82[EUR][1000 genomes]
rs6438562	0.86[EUR][1000 genomes]
rs6438564	0.87[EUR][1000 genomes]
rs6438566	0.87[EUR][1000 genomes]
rs6438567	0.87[EUR][1000 genomes]
rs6764549	0.87[EUR][1000 genomes]
rs6769988	0.91[EUR][1000 genomes]
rs6775625	0.81[EUR][1000 genomes]
rs6776122	0.87[EUR][1000 genomes]
rs6777971	0.80[EUR][1000 genomes]
rs6781470	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782570	0.93[EUR][1000 genomes]
rs6794478	0.93[EUR][1000 genomes]
rs6805050	0.87[EUR][1000 genomes]
rs7637828	0.87[EUR][1000 genomes]
rs7641838	0.87[EUR][1000 genomes]
rs7642171	0.86[EUR][1000 genomes]
rs7644268	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7653263	0.87[EUR][1000 genomes]
rs7653396	0.87[EUR][1000 genomes]
rs901920	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs902790	0.87[EUR][1000 genomes]
rs902791	0.87[EUR][1000 genomes]
rs902792	0.87[EUR][1000 genomes]
rs902794	0.87[EUR][1000 genomes]
rs902795	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs923380	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs923726	0.87[EUR][1000 genomes]
rs923727	0.87[EUR][1000 genomes]
rs923728	0.87[EUR][1000 genomes]
rs9289142	0.87[EUR][1000 genomes]
rs9289143	0.87[EUR][1000 genomes]
rs979682	0.87[EUR][1000 genomes]
rs9813834	0.87[EUR][1000 genomes]
rs9841122	0.87[EUR][1000 genomes]
rs9842302	0.87[EUR][1000 genomes]
rs9849023	0.83[EUR][1000 genomes]
rs9853082	0.87[EUR][1000 genomes]
rs9857123	0.87[EUR][1000 genomes]
rs9858566	0.87[EUR][1000 genomes]
rs9868058	0.84[EUR][1000 genomes]
rs9868312	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119836800-119860800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:119844200-119863400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:119854400-119863200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119854600-119863000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:119854800-119860800	Weak transcription	Hela-S3	cervix
6	chr3:119855000-119862600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:119856000-119862600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:119856600-119861000	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links