Variant report

Variant	rs2062377
Chromosome Location	chr8:120007420-120007421
allele	A/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	POLR2A	chr8:120007343-120007725	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr8:120007315-120007924	SK-N-SH	brain:	n/a	chr8:120007673-120007682 chr8:120007669-120007685
3	MEF2A	chr8:120007267-120007947	SK-N-SH	brain:	n/a	chr8:120007521-120007535 chr8:120007516-120007537 chr8:120007523-120007534 chr8:120007516-120007537
4	MEF2A	chr8:120007235-120007854	SK-N-SH	brain:	n/a	chr8:120007521-120007535 chr8:120007516-120007537 chr8:120007523-120007534 chr8:120007516-120007537

Variant related genes	Relation type
COLEC10	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10090576	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10505348	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10955915	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10955919	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11573824	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11573829	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11573885	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11992136	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11995824	0.89[EUR][1000 genomes]
rs12682278	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13254554	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13260214	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13262276	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13264172	0.82[EUR][1000 genomes]
rs13264791	0.83[AMR][1000 genomes]
rs1485289	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1485307	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1872426	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1905786	0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1982763	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2062375	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2062376	0.85[EUR][1000 genomes]
rs2073618	0.80[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2220189	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4242592	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4305930	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4307369	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4313185	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4319131	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4336637	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4354338	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4355805	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4397431	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4416847	0.85[EUR][1000 genomes]
rs4563920	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4567065	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4618726	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4876876	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6415470	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6469788	0.89[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs6469789	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6469792	0.85[EUR][1000 genomes]
rs6469794	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6469796	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6469798	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67819415	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6984287	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6984572	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6992497	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6996754	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6999476	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7006553	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7010043	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7010267	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs7013203	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7014574	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7016585	0.83[EUR][1000 genomes]
rs7463176	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7464496	0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7822098	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7824837	0.84[EUR][1000 genomes]
rs7838083	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7842942	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9969672	0.90[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv522241	chr8:119995697-120027871	Weak transcription Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Bone mineral density (spine)	19801982	GWAS catalog
Bone mineral density	23437003	GWAS catalog
Bone mineral density	22504420	GWAS catalog

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120006400-120008400	Enhancers	Fetal Heart	heart
2	chr8:120006800-120008000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:120006800-120008200	Enhancers	Osteobl	bone
4	chr8:120007000-120007800	Weak transcription	Right Ventricle	heart
5	chr8:120007000-120013600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr8:120007200-120008000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr8:120007200-120008000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr8:120007200-120008000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr8:120007200-120008000	Enhancers	NHLF	lung
10	chr8:120007200-120008400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:120007200-120008400	Enhancers	NH-A	brain
12	chr8:120007400-120007600	Enhancers	Sigmoid Colon	Sigmoid Colon

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