Variant report

Variant	rs10861567
Chromosome Location	chr12:106669526-106669527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106641409..106644539-chr12:106668096..106670238,5	MCF-7	breast:
2	chr12:106630802..106633610-chr12:106666760..106669656,2	MCF-7	breast:
3	chr12:106634944..106646449-chr12:106667585..106679535,27	MCF-7	breast:
4	chr12:106664388..106667969-chr12:106668032..106670678,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258355	Chromatin interaction
ENSG00000136026	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10507210	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746057	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778460	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10861569	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112924	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11112926	0.87[ASN][1000 genomes]
rs11112927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11112928	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1148408	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1148409	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1148410	0.96[ASN][1000 genomes]
rs1148411	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1148412	0.80[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1148442	0.91[ASN][1000 genomes]
rs1148443	0.95[ASN][1000 genomes]
rs1215808	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12230190	0.96[ASN][1000 genomes]
rs12823006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2047545	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2279760	0.81[JPT][hapmap]
rs7304941	0.81[JPT][hapmap]
rs7308143	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311121	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311133	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315560	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10861567	CKAP4	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106664800-106669600	Enhancers	Stomach Mucosa	stomach
2	chr12:106665600-106670200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:106665800-106670800	Weak transcription	Fetal Heart	heart
4	chr12:106666200-106680800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:106666400-106669600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr12:106666400-106670600	Weak transcription	NHEK	skin
7	chr12:106666600-106670400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr12:106666800-106670400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:106667400-106669600	Enhancers	Pancreas	Pancrea
10	chr12:106667600-106670400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:106667800-106669600	Enhancers	Fetal Intestine Large	intestine
12	chr12:106667800-106669600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr12:106668000-106669600	Enhancers	Colonic Mucosa	Colon
14	chr12:106668000-106669600	Enhancers	Fetal Intestine Small	intestine
15	chr12:106668200-106670200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr12:106668400-106671000	Enhancers	Esophagus	oesophagus
17	chr12:106668600-106669600	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr12:106668800-106670800	Enhancers	Primary B cells from peripheral blood	blood
19	chr12:106669200-106669600	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr12:106669200-106669600	Enhancers	Fetal Lung	lung
21	chr12:106669200-106669600	Enhancers	HepG2	liver
22	chr12:106669200-106670600	Flanking Active TSS	GM12878-XiMat	blood
23	chr12:106669400-106669600	Enhancers	Liver	Liver
24	chr12:106669400-106670200	Enhancers	Primary B cells from cord blood	blood
25	chr12:106669400-106670800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:106669400-106670800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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