Variant report

Variant	rs2782660
Chromosome Location	chr6:45687333-45687334
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	chr6:45389081..45390660-chr6:45685863..45688695,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12661654	0.82[CEU][hapmap]
rs1388242	0.81[CHB][hapmap]
rs1388244	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs1491139	0.83[AMR][1000 genomes]
rs1932040	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2396505	0.81[CHB][hapmap]
rs2637578	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2637580	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2782658	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]
rs2782659	0.95[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]
rs2782663	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2782666	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321321	0.84[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs321322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321324	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs321325	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4326224	0.81[CHB][hapmap]
rs4714864	0.83[AMR][1000 genomes]
rs6458458	0.81[AMR][1000 genomes]
rs9349324	0.82[AMR][1000 genomes]
rs9472552	0.81[CHB][hapmap]
rs9472557	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45682200-45690600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:45682800-45690400	Weak transcription	NHEK	skin
3	chr6:45684600-45690200	Weak transcription	HMEC	breast
4	chr6:45684800-45690200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:45685400-45687600	Enhancers	HSMM	muscle
6	chr6:45686000-45687400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:45686000-45687400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:45686000-45687400	Enhancers	NHDF-Ad	bronchial
9	chr6:45686000-45687600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr6:45686200-45687400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:45686200-45687600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:45686200-45687600	Enhancers	Osteobl	bone
13	chr6:45686800-45687400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:45687000-45690400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:45687200-45692400	Weak transcription	HSMMtube	muscle

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