Variant report

Variant	rs16908
Chromosome Location	chr1:86902807-86902808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:86902640-86902920	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86898686..86902993-chr1:86903541..86907633,5	K562	blood:

Variant related genes	Relation type
CLCA2	TF binding region
ENSG00000137975	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10782571	0.81[ASN][1000 genomes]
rs10873772	0.91[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10873773	0.81[ASN][1000 genomes]
rs10873775	0.81[ASN][1000 genomes]
rs10873776	0.81[ASN][1000 genomes]
rs10873778	0.91[CEU][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.82[ASN][1000 genomes]
rs1116108	0.91[CEU][hapmap]
rs1116109	0.84[ASN][1000 genomes]
rs11161805	0.81[ASN][1000 genomes]
rs11161807	0.81[ASN][1000 genomes]
rs11161811	0.85[ASN][1000 genomes]
rs11799437	0.95[CEU][hapmap]
rs11802019	0.87[CEU][hapmap]
rs11810689	0.81[ASN][1000 genomes]
rs12033867	0.82[ASN][1000 genomes]
rs12072655	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1407719	0.91[CEU][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1407720	0.81[ASN][1000 genomes]
rs1413427	0.96[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1413429	0.91[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17372196	0.91[CEU][hapmap];0.90[JPT][hapmap]
rs1999600	0.91[CEU][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2031136	0.81[ASN][1000 genomes]
rs2093612	0.82[ASN][1000 genomes]
rs2181418	0.80[ASN][1000 genomes]
rs2210641	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2273941	0.87[CEU][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2275001	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2390057	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs2390096	0.81[ASN][1000 genomes]
rs2390097	0.91[CEU][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.81[ASN][1000 genomes]
rs2390099	0.81[ASN][1000 genomes]
rs28782251	0.81[AFR][1000 genomes]
rs3737159	0.95[CEU][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3737672	0.91[CEU][hapmap];0.86[MEX][hapmap]
rs3765986	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3945233	0.95[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4534352	0.82[ASN][1000 genomes]
rs4656044	0.91[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs58200516	0.81[ASN][1000 genomes]
rs6674140	0.82[ASN][1000 genomes]
rs6703576	0.81[ASN][1000 genomes]
rs67799288	0.81[ASN][1000 genomes]
rs7415758	0.95[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7515651	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs7553685	0.86[CEU][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs956499	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]
rs9659676	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs969786	0.81[CHB][hapmap];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	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16908	GBP7	cis	cerebellum	SCAN
rs16908	ODF2L	cis	multi-tissue	Pritchard
rs16908	ODF2L	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86890600-86903000	Weak transcription	Esophagus	oesophagus
2	chr1:86896600-86914400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:86897200-86922800	Strong transcription	HMEC	breast
5	chr1:86897400-86906200	Strong transcription	NHEK	skin
6	chr1:86897400-86916000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:86902000-86913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:86902200-86905800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:86902200-86906800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:86902200-86907200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:86902400-86907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:86902400-86907400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:86902800-86903000	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links