Variant report

Variant	rs4743466
Chromosome Location	chr9:104275622-104275623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12350648	0.89[EUR][1000 genomes]
rs1929478	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1929485	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1929487	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28605156	0.88[EUR][1000 genomes]
rs2900310	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818337	0.83[CHB][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription 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	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743466	SEC61B	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104270800-104276000	Weak transcription	Adipose Nuclei	Adipose
2	chr9:104271000-104276000	Weak transcription	NHEK	skin
3	chr9:104271600-104276000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:104272200-104276400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:104273400-104277400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr9:104273800-104275800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:104274000-104275800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:104274000-104277200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:104274000-104277200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:104274000-104277200	Enhancers	Osteobl	bone
11	chr9:104274000-104277400	Enhancers	NHDF-Ad	bronchial
12	chr9:104274000-104277600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr9:104274000-104277600	Enhancers	NHLF	lung
14	chr9:104274000-104277800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr9:104274200-104277200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr9:104274200-104277200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:104274200-104277200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:104274600-104275800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:104274600-104277200	Enhancers	HSMM	muscle
20	chr9:104274600-104277600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr9:104274800-104276000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:104274800-104276000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:104275000-104276800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:104275000-104276800	Weak transcription	Pancreas	Pancrea
25	chr9:104275400-104277200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:104275400-104277400	Enhancers	Brain Anterior Caudate	brain
27	chr9:104275400-104277600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr9:104275600-104276000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:104275600-104276200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:104275600-104276200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr9:104275600-104276200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr9:104275600-104276200	Weak transcription	Aorta	Aorta
33	chr9:104275600-104276400	Flanking Active TSS	Fetal Heart	heart
34	chr9:104275600-104277400	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links