Variant report

Variant	rs4743827
Chromosome Location	chr9:92823544-92823545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:92816435..92819460-chr9:92821630..92825656,3	MCF-7	breast:
2	chr9:92820911..92823641-chr9:92827194..92830038,2	MCF-7	breast:
3	chr9:92219096..92220689-chr9:92821073..92823760,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10118926	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10122211	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1036701	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs10820826	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10991697	0.94[JPT][hapmap]
rs10991831	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10991907	0.83[JPT][hapmap]
rs1443361	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1443362	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1571447	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1887903	0.83[AMR][1000 genomes]
rs2028630	0.85[AMR][1000 genomes]
rs4142061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743823	0.90[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4743824	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744020	0.94[JPT][hapmap]
rs4744040	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]
rs6479330	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7021437	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7027342	0.81[ASN][1000 genomes]
rs7030563	0.90[CHB][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs894636	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs920753	0.81[ASN][1000 genomes]
rs920754	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs993171	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	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
4	nsv893563	chr9:92816727-92967125	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743827	SYK	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92815600-92823600	Weak transcription	Gastric	stomach
2	chr9:92817800-92826000	Weak transcription	Liver	Liver
3	chr9:92822600-92824400	Enhancers	Pancreas	Pancrea
4	chr9:92822800-92824600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr9:92823000-92824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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