Variant report

Variant	rs6930292
Chromosome Location	chr6:117783770-117783771
allele	G/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	chr6:117783298-117783824	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr6:117783109-117783862	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RNU6-253P	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs13192511	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13193572	0.88[JPT][hapmap]
rs13195478	0.83[JPT][hapmap]
rs13195673	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs13196791	0.86[ASN][1000 genomes]
rs13198016	0.86[ASN][1000 genomes]
rs13198224	0.80[ASN][1000 genomes]
rs13202267	0.86[ASN][1000 genomes]
rs13202333	0.85[ASN][1000 genomes]
rs13202514	0.82[ASN][1000 genomes]
rs13205723	0.86[ASN][1000 genomes]
rs13205753	0.87[ASN][1000 genomes]
rs13205986	0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs13206063	0.88[ASN][1000 genomes]
rs13207962	0.84[JPT][hapmap]
rs13208369	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13210963	0.82[JPT][hapmap]
rs13211956	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13212002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217856	0.86[ASN][1000 genomes]
rs13218378	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1407181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17079188	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs17079281	0.89[JPT][hapmap]
rs1853146	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1853147	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885064	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2104064	0.89[JPT][hapmap]
rs2273601	0.89[JPT][hapmap];0.89[LWK][hapmap];0.82[YRI][hapmap]
rs34059490	0.89[ASN][1000 genomes]
rs34331459	0.86[ASN][1000 genomes]
rs35002781	0.86[ASN][1000 genomes]
rs36045731	0.89[ASN][1000 genomes]
rs3777980	0.89[JPT][hapmap]
rs3777982	0.89[JPT][hapmap]
rs4632931	0.86[ASN][1000 genomes]
rs62433102	0.86[ASN][1000 genomes]
rs62433108	0.84[ASN][1000 genomes]
rs6568976	0.86[ASN][1000 genomes]
rs6568977	0.86[ASN][1000 genomes]
rs6568978	0.86[ASN][1000 genomes]
rs6568979	0.86[ASN][1000 genomes]
rs6910338	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6936540	0.86[ASN][1000 genomes]
rs6940327	0.92[ASN][1000 genomes]
rs6941824	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6942067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722359	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7739294	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7745840	0.86[ASN][1000 genomes]
rs7746536	0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7749229	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756187	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7763979	0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7764024	0.86[ASN][1000 genomes]
rs9481719	0.83[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9489152	0.90[JPT][hapmap]
rs9489155	0.84[AFR][1000 genomes]
rs9489157	0.83[AFR][1000 genomes]
rs9489166	0.87[AFR][1000 genomes]
rs9489173	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9489193	0.94[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9489199	0.80[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6930292	GOPC	cis	parietal	SCAN
rs6930292	DCBLD1	cis	Thyroid	GTEx
rs6930292	FRK	cis	cerebellum	SCAN
rs6930292	DCBLD1	cis	parietal	SCAN
rs6930292	DCBLD1	cis	Whole Blood	GTEx
rs6930292	MCM9	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117781000-117785000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:117782400-117784600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:117783400-117784000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:117783600-117783800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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