Variant report

Variant	rs6870835
Chromosome Location	chr5:44514648-44514649
allele	A/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	STAT3	chr5:44514555-44514809	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000249203	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10061166	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10062760	0.83[EUR][1000 genomes]
rs10941672	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10941673	0.89[EUR][1000 genomes]
rs1116180	0.91[EUR][1000 genomes]
rs12186589	0.90[EUR][1000 genomes]
rs12188017	0.94[EUR][1000 genomes]
rs12188390	0.89[EUR][1000 genomes]
rs13355269	0.90[EUR][1000 genomes]
rs13358061	0.86[EUR][1000 genomes]
rs1482695	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1531803	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1552184	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16901868	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17319592	0.93[EUR][1000 genomes]
rs1871950	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2128431	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2330570	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs28561538	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56313556	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57777873	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58261355	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58826391	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60912459	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61399521	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6451764	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6869262	0.87[EUR][1000 genomes]
rs6884170	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72748041	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72748047	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72748048	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72748056	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72748063	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72748065	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72748076	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72748082	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72748092	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72750279	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73752037	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7733376	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs922853	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs922854	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs922855	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs957739	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv830277	chr5:44383402-44566881	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1024923	chr5:44439853-44528314	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3469179	chr5:44514137-44517946	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	esv3469180	chr5:44514212-44517894	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	esv3469181	chr5:44514212-44517894	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6870835	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44512000-44525600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:44513000-44514800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:44513800-44515800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:44514000-44515200	Weak transcription	Ovary	ovary
5	chr5:44514400-44515200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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