Variant report

Variant	rs9846102
Chromosome Location	chr3:51879687-51879688
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	chr3:51878113..51880884-chr3:51974906..51977632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10433610	1.00[JPT][hapmap]
rs13325762	0.92[AFR][1000 genomes]
rs1857801	0.92[AFR][1000 genomes]
rs2102297	0.84[EUR][1000 genomes]
rs28776255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28799908	0.81[EUR][1000 genomes]
rs28874597	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280629	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4687780	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55668803	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58932899	0.84[EUR][1000 genomes]
rs61011489	0.84[AFR][1000 genomes]
rs61048512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61299098	0.93[AFR][1000 genomes]
rs6446041	0.86[EUR][1000 genomes]
rs6765123	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6781310	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789601	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792143	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6803994	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806593	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs6806812	0.91[AFR][1000 genomes]
rs73838712	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7623760	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632944	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs7635409	1.00[CEU][hapmap]
rs7639080	0.86[EUR][1000 genomes]
rs975258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815475	0.85[YRI][hapmap]
rs9822619	0.84[AFR][1000 genomes]
rs9822994	0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs9823975	0.93[AFR][1000 genomes]
rs9831594	0.92[AFR][1000 genomes]
rs9839703	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840747	0.84[AFR][1000 genomes]
rs9840833	0.86[EUR][1000 genomes]
rs9856180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856660	0.84[EUR][1000 genomes]
rs9858279	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs9859656	0.82[YRI][hapmap]
rs9859820	0.88[AFR][1000 genomes]
rs9863019	0.82[AFR][1000 genomes]
rs9867269	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867278	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9874046	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9874547	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9875459	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9876690	0.84[EUR][1000 genomes]
rs9877178	0.81[AFR][1000 genomes]
rs9878564	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9880623	0.84[AFR][1000 genomes]
rs9880628	1.00[CEU][hapmap]
rs9880631	0.84[AFR][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv3416846	chr3:51781117-51888179	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv1001350	chr3:51860817-51899966	Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51878600-51880200	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr3:51878600-51880400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr3:51878800-51880000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:51878800-51880000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:51878800-51880200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:51879200-51880000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:51879600-51880000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:51879600-51880200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr3:51879600-51881400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links