Variant report

Variant	rs9842330
Chromosome Location	chr3:81814688-81814689
allele	A/G
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	RUNX3	chr3:81814535-81815036	GM12878	blood:	n/a	n/a
2	RUNX3	chr3:81814600-81814932	GM12878	blood:	n/a	n/a
3	IKZF1	chr3:81814646-81814780	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000242190	TF binding region
GBE1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11711331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11712243	0.87[EUR][1000 genomes]
rs11915042	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13074632	0.86[EUR][1000 genomes]
rs13083476	0.87[EUR][1000 genomes]
rs13088000	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464791	0.80[EUR][1000 genomes]
rs2290081	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2873054	0.81[EUR][1000 genomes]
rs34692099	0.82[AMR][1000 genomes]
rs3755713	0.87[EUR][1000 genomes]
rs3772882	0.84[EUR][1000 genomes]
rs3772883	0.84[EUR][1000 genomes]
rs3772884	0.87[EUR][1000 genomes]
rs3860595	0.84[EUR][1000 genomes]
rs4411908	0.84[EUR][1000 genomes]
rs6548773	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6765917	0.81[EUR][1000 genomes]
rs7641973	0.80[EUR][1000 genomes]
rs9817181	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9818006	0.84[EUR][1000 genomes]
rs9826270	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9842330	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81811200-81818200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:81811400-81818200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:81811800-81814800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:81811800-81818200	Weak transcription	Osteobl	bone
5	chr3:81811800-81818600	Weak transcription	NHEK	skin
6	chr3:81813200-81815400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:81813400-81814800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:81813400-81814800	Enhancers	HSMM	muscle
9	chr3:81813600-81814800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:81813600-81815000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:81814200-81814800	Enhancers	HSMMtube	muscle
12	chr3:81814400-81815000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:81814600-81814800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:81814600-81814800	Enhancers	HUES6 Cell Line	embryonic stem cell

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