Variant report

Variant	rs657867
Chromosome Location	chr9:27108975-27108976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10738763	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs10967715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967716	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967722	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2782416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2782430	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3904612	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55996435	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615375	0.83[TSI][hapmap]
rs630023	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651031	0.87[ASN][1000 genomes]
rs677534	0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs679026	1.00[JPT][hapmap]
rs680739	0.95[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs681182	0.95[CEU][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72713704	0.90[ASN][1000 genomes]
rs72713707	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs657867	TEK	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27096800-27109000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:27108200-27109000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr9:27108400-27109000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr9:27108600-27109000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:27108600-27109000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr9:27108600-27109000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:27108600-27109600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:27108600-27111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr9:27108800-27109000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:27108800-27109000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr9:27108800-27109000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:27108800-27109000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr9:27108800-27109000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:27108800-27109000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr9:27108800-27109000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:27108800-27109000	Enhancers	Fetal Lung	lung
17	chr9:27108800-27109000	Enhancers	Fetal Muscle Leg	muscle
18	chr9:27108800-27109000	Active TSS	Ovary	ovary
19	chr9:27108800-27109000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:27108800-27109000	Enhancers	NH-A	brain
21	chr9:27108800-27109200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:27108800-27109200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr9:27108800-27109200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr9:27108800-27109200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr9:27108800-27109200	Active TSS	Adipose Nuclei	Adipose
26	chr9:27108800-27109200	Enhancers	Fetal Stomach	stomach
27	chr9:27108800-27109400	Active TSS	NHDF-Ad	bronchial
28	chr9:27108800-27109600	Flanking Active TSS	HUVEC	blood vessel
29	chr9:27108800-27109600	Enhancers	NHLF	lung
30	chr9:27108800-27109800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr9:27108800-27109800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:27108800-27109800	Flanking Active TSS	Osteobl	bone
33	chr9:27108800-27110000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:27108800-27110600	Active TSS	H1 Cell Line	embryonic stem cell
35	chr9:27108800-27111600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr9:27108800-27111800	Active TSS	Right Atrium	heart
37	chr9:27108800-27112000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links