Variant report

Variant	rs28490262
Chromosome Location	chr3:80814042-80814043
allele	C/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	chr3:80814001-80814376	MCF10A-Er-Src	breast:	n/a	chr3:80814348-80814356

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ROBO2-4	chr3:80813985-80814238	XLOC_002716

Variant related genes	Relation type
ENSG00000242781	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12485625	0.87[AMR][1000 genomes]
rs13078405	0.84[EUR][1000 genomes]
rs1320910	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13318177	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13324031	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1437046	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1516585	0.84[EUR][1000 genomes]
rs1520589	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520590	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17280627	0.82[AFR][1000 genomes]
rs1996224	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2037094	0.83[EUR][1000 genomes]
rs2049778	0.83[EUR][1000 genomes]
rs2056084	0.81[EUR][1000 genomes]
rs2139685	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176029	0.83[EUR][1000 genomes]
rs2372654	0.83[EUR][1000 genomes]
rs2372655	0.83[EUR][1000 genomes]
rs28717382	0.83[AMR][1000 genomes]
rs28885819	0.89[AFR][1000 genomes]
rs4270470	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs500298	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs528897	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs571776	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs584597	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs588001	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs613707	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs619305	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62258009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62258010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs627529	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6548716	0.84[EUR][1000 genomes]
rs6548719	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs704464	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7431461	0.83[EUR][1000 genomes]
rs7617921	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621792	0.84[EUR][1000 genomes]
rs7630983	0.84[EUR][1000 genomes]
rs7630997	0.83[EUR][1000 genomes]
rs7633466	0.84[EUR][1000 genomes]
rs7633748	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7639808	0.87[AMR][1000 genomes]
rs7643304	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs878245	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs966619	0.84[EUR][1000 genomes]
rs9818650	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832758	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004115	chr3:80349665-81043308	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv536601	chr3:80349665-81043308	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1067580	chr3:80416729-81043307	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv492220	chr3:80416729-81043307	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1000592	chr3:80422155-81044175	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv527598	chr3:80585455-81250663	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv877038	chr3:80781726-80984958	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1846627	chr3:80791380-80912454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:80803800-80817200	Weak transcription	Placenta	Placenta
2	chr3:80804000-80816400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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