Variant report

Variant	rs1115159
Chromosome Location	chr6:54753541-54753542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54711519..54714524-chr6:54749320..54755101,5	MCF-7	breast:
2	chr6:54713425..54714965-chr6:54753003..54756000,2	MCF-7	breast:
3	chr6:54751952..54753804-chr6:54753869..54755428,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10485136	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12525787	0.82[ASN][1000 genomes]
rs12662124	0.82[ASN][1000 genomes]
rs1393776	0.82[CHB][hapmap]
rs148109	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1503147	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1963697	0.82[CHB][hapmap]
rs2064432	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2143798	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2179786	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs239850	0.82[ASN][1000 genomes]
rs239854	0.82[ASN][1000 genomes]
rs2816811	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4141552	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4712081	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6908170	0.82[ASN][1000 genomes]
rs6926997	0.82[CHB][hapmap]
rs72645372	0.82[ASN][1000 genomes]
rs7382364	0.82[ASN][1000 genomes]
rs7453866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741915	0.95[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7746374	0.82[ASN][1000 genomes]
rs7772421	0.81[ASN][1000 genomes]
rs7774660	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9296771	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs932452	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs9349740	0.82[CHB][hapmap]
rs9367597	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9367608	0.82[CHB][hapmap]
rs9370332	0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs9370333	0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs9370336	0.81[AMR][1000 genomes]
rs9370337	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370345	0.82[CHB][hapmap]
rs9382390	0.82[ASN][1000 genomes]
rs9382397	0.82[ASN][1000 genomes]
rs9382403	0.82[CHB][hapmap]
rs9382442	0.81[CHB][hapmap]
rs9396006	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9396036	0.93[CHB][hapmap]
rs9475068	0.82[ASN][1000 genomes]
rs9475081	0.82[ASN][1000 genomes]
rs960835	0.80[ASN][1000 genomes]
rs988913	0.82[CHB][hapmap]
rs995851	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54737600-54755800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
3	chr6:54744200-54757600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:54744800-54755800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:54746200-54755200	Weak transcription	NHEK	skin
7	chr6:54746200-54755600	Weak transcription	HMEC	breast
8	chr6:54746400-54757800	Weak transcription	Hela-S3	cervix
9	chr6:54747600-54756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:54752200-54759000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:54752400-54758600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:54753400-54754200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links