Variant report

Variant	rs12662574
Chromosome Location	chr6:55757305-55757306
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	chr11:62608926..62610622-chr6:55755825..55757569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10485079	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10498807	0.96[ASN][1000 genomes]
rs12190955	0.93[ASN][1000 genomes]
rs12193440	0.93[ASN][1000 genomes]
rs12196975	0.96[ASN][1000 genomes]
rs12197097	0.96[ASN][1000 genomes]
rs12202960	0.96[ASN][1000 genomes]
rs12204345	0.93[ASN][1000 genomes]
rs12209008	0.96[ASN][1000 genomes]
rs12209061	0.96[ASN][1000 genomes]
rs12210486	0.96[ASN][1000 genomes]
rs12210591	0.96[ASN][1000 genomes]
rs12210906	0.96[ASN][1000 genomes]
rs12211480	0.86[ASN][1000 genomes]
rs12215767	0.96[ASN][1000 genomes]
rs12215768	0.96[ASN][1000 genomes]
rs12660631	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374542	0.96[ASN][1000 genomes]
rs1374546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1447130	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16887320	0.82[AMR][1000 genomes]
rs16887333	0.82[AMR][1000 genomes]
rs16887397	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16887398	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16887399	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16887402	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17736107	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1868033	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1900526	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1900527	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084290	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2100105	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2100107	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2197643	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2397191	0.96[ASN][1000 genomes]
rs2397194	0.96[ASN][1000 genomes]
rs3798819	0.89[JPT][hapmap]
rs3798821	0.82[AMR][1000 genomes]
rs4623244	0.96[ASN][1000 genomes]
rs5007842	0.89[ASN][1000 genomes]
rs59418534	0.96[ASN][1000 genomes]
rs6908374	0.93[ASN][1000 genomes]
rs6909631	0.96[ASN][1000 genomes]
rs6910852	0.98[ASN][1000 genomes]
rs6915768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6927010	0.96[ASN][1000 genomes]
rs6927212	0.96[ASN][1000 genomes]
rs6927427	0.96[ASN][1000 genomes]
rs6928174	0.93[ASN][1000 genomes]
rs6928604	0.93[ASN][1000 genomes]
rs6928783	0.93[ASN][1000 genomes]
rs6931303	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6931309	0.98[ASN][1000 genomes]
rs6931324	0.98[ASN][1000 genomes]
rs6931472	0.98[ASN][1000 genomes]
rs6935710	0.98[ASN][1000 genomes]
rs6935907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7453408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9382566	0.96[ASN][1000 genomes]
rs9382567	0.96[ASN][1000 genomes]
rs9382568	0.84[ASN][1000 genomes]
rs9396162	0.96[ASN][1000 genomes]
rs9475448	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]
rs9475450	0.98[ASN][1000 genomes]
rs9475451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475452	0.96[ASN][1000 genomes]
rs9475453	0.96[ASN][1000 genomes]
rs9968834	0.96[ASN][1000 genomes]
rs9969009	0.96[ASN][1000 genomes]
rs9969010	0.96[ASN][1000 genomes]
rs9969100	0.96[ASN][1000 genomes]
rs9969103	0.96[ASN][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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2752670	chr6:55614978-55781605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1032684	chr6:55680473-55766876	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024174	chr6:55713889-55829936	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1029301	chr6:55713889-55834480	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv830665	chr6:55755560-55920219	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55757200-55758000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links