Variant report

Variant	rs10009242
Chromosome Location	chr4:104293598-104293599
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	GATA3	chr4:104293174-104293905	SK-N-SH	brain:	n/a	n/a
2	FOS	chr4:104293525-104293677	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr4:104293240-104293769	HUVEC	blood vessel:	n/a	n/a
4	GATA3	chr4:104293252-104293866	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr4:104293299-104293848	SK-N-SH	brain:	n/a	n/a
6	GATA2	chr4:104293249-104293837	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000248740	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10212959	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1156669	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734572	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356293	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1400365	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1516740	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1607094	0.83[ASN][1000 genomes]
rs1607095	0.83[ASN][1000 genomes]
rs2138592	0.91[ASN][1000 genomes]
rs28397882	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28498687	0.98[ASN][1000 genomes]
rs2866645	0.82[ASN][1000 genomes]
rs28728298	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4481237	0.91[ASN][1000 genomes]
rs6533082	0.82[ASN][1000 genomes]
rs6533083	0.82[ASN][1000 genomes]
rs6533088	0.93[ASN][1000 genomes]
rs6821137	0.84[ASN][1000 genomes]
rs6822783	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6828151	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6828829	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6836157	0.84[ASN][1000 genomes]
rs6855777	0.84[ASN][1000 genomes]
rs7699661	0.85[ASN][1000 genomes]
rs951598	0.97[ASN][1000 genomes]
rs970156	0.81[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	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2757947	chr4:104179925-104342395	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2759271	chr4:104179925-104342395	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3348747	chr4:104214627-104609795	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv879686	chr4:104260725-104335667	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv879687	chr4:104288620-104371785	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10009242	TET2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104282200-104293600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:104283800-104296400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:104286400-104293800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:104287000-104295000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:104292000-104293600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:104292000-104294000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:104292000-104295400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:104292200-104295200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:104292800-104294200	Enhancers	HUVEC	blood vessel
10	chr4:104293400-104294200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:104293400-104294400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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