Variant report

Variant	rs6828829
Chromosome Location	chr4:104335667-104335668
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	chr4:104333746..104335920-chr4:104344875..104346775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248740	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10009242	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10212959	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1156669	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734572	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11946500	0.92[AFR][1000 genomes]
rs1356293	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1400365	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1516740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1607094	0.81[ASN][1000 genomes]
rs1607095	0.81[ASN][1000 genomes]
rs2138592	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28397882	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28498687	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615487	0.92[AFR][1000 genomes]
rs2866645	0.80[EUR][1000 genomes]
rs28728298	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4481237	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699071	0.80[AFR][1000 genomes]
rs6533082	0.80[EUR][1000 genomes]
rs6533083	0.80[EUR][1000 genomes]
rs6533088	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821137	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6822783	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6828151	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836157	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6855777	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7699661	0.84[ASN][1000 genomes]
rs951598	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2757947	chr4:104179925-104342395	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2759271	chr4:104179925-104342395	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3348747	chr4:104214627-104609795	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv879686	chr4:104260725-104335667	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv879687	chr4:104288620-104371785	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv830023	chr4:104333042-104522801	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104333600-104338600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:104334800-104336600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:104334800-104343800	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links