Variant report

Variant	rs4744040
Chromosome Location	chr9:92806474-92806475
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	TCF12	chr9:92806402-92807627	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000227555	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10118926	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10122211	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1036701	0.80[EUR][1000 genomes]
rs10820817	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10820826	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10991697	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10991831	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1443361	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1443362	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17361084	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4142061	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4743823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743827	0.90[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744020	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6479330	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021437	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027342	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7030563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894636	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs920753	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs993171	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv893562	chr9:92794721-92850878	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4744040	CKS2	cis	cerebellum	SCAN
rs4744040	SYK	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92800000-92807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:92806000-92806600	Enhancers	Hela-S3	cervix
3	chr9:92806000-92807000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:92806200-92806600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:92806200-92806600	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr9:92806200-92806600	Enhancers	HUVEC	blood vessel
7	chr9:92806200-92807400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:92806200-92807400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:92806200-92807400	Enhancers	Gastric	stomach
10	chr9:92806400-92807200	Weak transcription	Lung	lung
11	chr9:92806400-92807600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:92806400-92807600	Flanking Active TSS	A549	lung
13	chr9:92806400-92808200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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