Variant report

Variant	rs13198555
Chromosome Location	chr6:11397982-11397983
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11396064..11399493-chr6:11408571..11410714,3	MCF-7	breast:
2	chr6:11355160..11356813-chr6:11395233..11398054,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1012502	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1013678	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947204	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12193099	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12199545	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12204242	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12208626	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12210644	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12215372	0.96[CEU][hapmap];0.81[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs12215715	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12215894	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13217274	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1810451	0.82[EUR][1000 genomes]
rs3798752	0.81[GIH][hapmap]
rs4276494	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4330532	0.82[AMR][1000 genomes]
rs4370358	0.82[AMR][1000 genomes]
rs4533978	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4632886	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711271	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711272	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5019594	0.82[CHB][hapmap]
rs6901388	0.84[AMR][1000 genomes]
rs6904848	0.81[AMR][1000 genomes]
rs6908442	0.81[AMR][1000 genomes]
rs6916534	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918440	0.82[CHB][hapmap]
rs6919269	0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs6931599	0.81[AMR][1000 genomes]
rs6932496	0.96[CEU][hapmap];0.81[CHB][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs7738560	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7751151	0.82[AMR][1000 genomes]
rs7752735	0.82[AMR][1000 genomes]
rs7766220	0.84[AMR][1000 genomes]
rs7768351	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296000	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs9348868	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9357127	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9366788	0.82[AMR][1000 genomes]
rs9368701	0.89[ASN][1000 genomes]
rs9461714	0.91[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs9469034	0.88[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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13198555	C6orf218	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11393600-11398000	Weak transcription	Lung	lung
2	chr6:11393600-11398600	Weak transcription	Adipose Nuclei	Adipose
3	chr6:11393800-11398000	Weak transcription	Liver	Liver
4	chr6:11394000-11398000	Enhancers	HepG2	liver
5	chr6:11394000-11405600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:11394200-11398000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:11394200-11398000	Weak transcription	Spleen	Spleen
8	chr6:11394200-11398800	Weak transcription	Fetal Lung	lung
9	chr6:11394800-11398000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:11394800-11398600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:11394800-11398600	Weak transcription	Fetal Kidney	kidney
12	chr6:11394800-11403600	Weak transcription	Primary B cells from cord blood	blood
13	chr6:11395000-11398600	Weak transcription	A549	lung
14	chr6:11395000-11398800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:11395200-11398800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:11395800-11398000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:11396000-11398000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:11396000-11398400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:11397400-11400200	Enhancers	Fetal Intestine Large	intestine
20	chr6:11397600-11400000	Enhancers	Fetal Intestine Small	intestine
21	chr6:11397800-11399600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr6:11397800-11400000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links