Variant report

Variant	rs1366840
Chromosome Location	chr2:185767854-185767855
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	STAT3	chr2:185767725-185767925	MCF10A-Er-Src	breast:	n/a	chr2:185767871-185767882

Variant related genes	Relation type
ENSG00000237824	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10210216	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10931156	0.88[CHB][hapmap];0.81[CHD][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap]
rs11901504	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12476147	0.88[CHB][hapmap]
rs13025111	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13026742	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13388087	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13401381	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1344707	1.00[JPT][hapmap]
rs1366838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1366839	1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs1366842	0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs1429427	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1583049	0.87[CHB][hapmap]
rs17431742	1.00[CEU][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap]
rs1835172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2059923	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2059924	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2170203	0.85[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2369595	1.00[JPT][hapmap]
rs4666994	1.00[JPT][hapmap]
rs4666995	1.00[JPT][hapmap]
rs4666998	1.00[JPT][hapmap]
rs4667000	0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4667001	0.81[AMR][1000 genomes]
rs56213902	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6726421	0.88[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs725617	1.00[JPT][hapmap]
rs7590852	1.00[JPT][hapmap]
rs7594906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7603001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532412	chr2:185347334-186108701	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv520974	chr2:185742474-186148230	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv821846	chr2:185753228-185774831	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
4	nsv818104	chr2:185756082-185771745	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
5	nsv517466	chr2:185756082-185778262	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1366840	FSIP2	cis	cerebellum	SCAN
rs1366840	CALCRL	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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