Variant report

Variant	rs9475046
Chromosome Location	chr6:54720275-54720276
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54582865..54585119-chr6:54718425..54721186,2	MCF-7	breast:
2	chr6:54718981..54722041-chr6:54724023..54729682,8	MCF-7	breast:
3	chr6:54718921..54722891-chr6:54723074..54726787,4	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10807484	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10807485	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948862	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10948864	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191299	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12191386	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194667	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12195438	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196314	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs12201892	0.86[ASN][1000 genomes]
rs12202062	0.86[ASN][1000 genomes]
rs12203709	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.99[ASN][1000 genomes]
rs12205222	0.92[ASN][1000 genomes]
rs12205372	0.94[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12207559	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12216039	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12216049	0.98[ASN][1000 genomes]
rs1910357	0.99[ASN][1000 genomes]
rs2270989	0.99[ASN][1000 genomes]
rs34713378	0.84[ASN][1000 genomes]
rs4712075	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62412605	0.85[ASN][1000 genomes]
rs6908745	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6911198	0.84[CHB][hapmap];0.96[CHD][hapmap];0.82[MEX][hapmap]
rs72957572	0.85[ASN][1000 genomes]
rs7747352	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760490	0.87[ASN][1000 genomes]
rs9296769	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9464148	0.98[ASN][1000 genomes]
rs9464149	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475001	0.82[CEU][hapmap]
rs9475029	0.86[ASN][1000 genomes]
rs9475038	0.98[ASN][1000 genomes]
rs9475039	0.99[ASN][1000 genomes]
rs9475040	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475041	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475045	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9475046	ICK	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54712600-54725000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:54713200-54720800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:54713200-54721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:54713200-54725600	Weak transcription	Gastric	stomach
5	chr6:54713400-54720800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:54713400-54720800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:54713400-54726400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:54714800-54720400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:54715400-54720800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:54715400-54731200	Weak transcription	Hela-S3	cervix
11	chr6:54717400-54720400	Weak transcription	Stomach Mucosa	stomach
12	chr6:54717600-54720400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:54718600-54720400	Weak transcription	Fetal Intestine Large	intestine
14	chr6:54718600-54720800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:54719400-54720800	Strong transcription	HMEC	breast
16	chr6:54719400-54720800	Genic enhancers	NHEK	skin
17	chr6:54720200-54720400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:54720200-54720800	Enhancers	Duodenum Mucosa	Duodenum
19	chr6:54720200-54721200	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr6:54720200-54721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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