Variant report

Variant	rs1859443
Chromosome Location	chr12:48399612-48399613
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	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a
2	CTBP2	chr12:48397798-48399716	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48392370..48394722-chr12:48397446..48401400,3	K562	blood:
2	chr12:48399203..48400811-chr12:48412734..48415114,2	K562	blood:
3	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:
4	chr12:48399203..48401006-chr12:48440249..48442960,2	K562	blood:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1049392	0.94[JPT][hapmap]
rs10747529	0.94[JPT][hapmap]
rs10875733	0.94[JPT][hapmap]
rs10875739	0.94[JPT][hapmap]
rs10875752	0.94[JPT][hapmap]
rs10875754	0.94[JPT][hapmap]
rs10875761	0.94[JPT][hapmap]
rs10875766	0.94[JPT][hapmap]
rs11168350	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168353	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168354	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168358	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168363	0.94[JPT][hapmap]
rs11168364	0.94[JPT][hapmap]
rs11168373	0.94[JPT][hapmap]
rs11168404	0.94[JPT][hapmap]
rs11168417	0.94[JPT][hapmap]
rs11168424	0.93[JPT][hapmap]
rs11168434	0.94[JPT][hapmap]
rs11168435	0.94[JPT][hapmap]
rs11168438	0.91[JPT][hapmap]
rs11168445	0.94[JPT][hapmap]
rs11168448	0.94[JPT][hapmap]
rs11168453	0.94[JPT][hapmap]
rs11168454	0.94[JPT][hapmap]
rs12422355	0.94[JPT][hapmap]
rs12423250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1635527	0.96[YRI][hapmap]
rs17122567	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1793958	0.83[JPT][hapmap]
rs1793960	0.88[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1859442	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2286020	0.94[JPT][hapmap]
rs2408954	0.94[JPT][hapmap]
rs3742075	0.87[JPT][hapmap]
rs3825403	0.94[JPT][hapmap]
rs4258439	0.94[JPT][hapmap]
rs58086963	0.81[ASN][1000 genomes]
rs7299704	0.94[JPT][hapmap]
rs7302354	0.94[JPT][hapmap]
rs7303677	0.94[JPT][hapmap]
rs7484942	0.94[JPT][hapmap]
rs765260	0.94[JPT][hapmap]
rs7962390	0.94[JPT][hapmap]
rs7962569	0.87[JPT][hapmap]
rs8181670	0.94[JPT][hapmap]
rs886589	0.94[JPT][hapmap]
rs954326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9651981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9669263	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9804751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48397800-48399800	Bivalent Enhancer	Fetal Lung	lung
2	chr12:48399000-48399800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
3	chr12:48399000-48400200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:48399200-48400000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:48399200-48400200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:48399400-48399800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48399400-48399800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr12:48399400-48400000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:48399400-48400000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
11	chr12:48399600-48399800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
12	chr12:48399600-48399800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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