Variant report

Variant	rs6899820
Chromosome Location	chr6:11476635-11476636
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11472497..11474749-chr6:11475109..11477785,2	MCF-7	breast:
2	chr6:11465282..11468042-chr6:11475688..11477880,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10807114	0.81[ASN][1000 genomes]
rs10807115	0.81[ASN][1000 genomes]
rs11751884	0.80[ASN][1000 genomes]
rs11755780	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11756371	0.80[ASN][1000 genomes]
rs12192094	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12198765	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12198774	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12198950	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12200391	0.81[ASN][1000 genomes]
rs12200454	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1923525	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2025184	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2025185	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4711303	0.83[CEU][hapmap]
rs4711306	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4713593	0.84[ASN][1000 genomes]
rs4713594	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4713618	0.87[JPT][hapmap]
rs480684	0.85[EUR][1000 genomes]
rs486127	0.85[EUR][1000 genomes]
rs487729	0.83[EUR][1000 genomes]
rs490327	0.85[EUR][1000 genomes]
rs518183	0.82[EUR][1000 genomes]
rs528012	0.83[EUR][1000 genomes]
rs528087	0.84[EUR][1000 genomes]
rs533319	0.85[EUR][1000 genomes]
rs562508	0.85[EUR][1000 genomes]
rs568867	0.83[EUR][1000 genomes]
rs570714	0.83[EUR][1000 genomes]
rs575164	0.84[EUR][1000 genomes]
rs588062	0.86[JPT][hapmap]
rs588948	0.83[EUR][1000 genomes]
rs595877	0.87[JPT][hapmap]
rs601505	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs609135	0.83[EUR][1000 genomes]
rs61570488	0.88[ASN][1000 genomes]
rs617157	0.83[EUR][1000 genomes]
rs618998	0.85[EUR][1000 genomes]
rs620867	0.83[EUR][1000 genomes]
rs623024	0.84[EUR][1000 genomes]
rs671048	0.85[EUR][1000 genomes]
rs681483	0.91[JPT][hapmap]
rs6901328	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6904400	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6907796	0.81[ASN][1000 genomes]
rs6913697	0.84[ASN][1000 genomes]
rs6914208	0.80[ASN][1000 genomes]
rs6914420	0.84[ASN][1000 genomes]
rs6915153	0.84[ASN][1000 genomes]
rs6915366	0.84[ASN][1000 genomes]
rs6926422	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6940859	0.87[ASN][1000 genomes]
rs6941011	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6941700	0.84[ASN][1000 genomes]
rs9348892	0.84[ASN][1000 genomes]
rs9348895	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9348896	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9357150	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357154	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9366805	0.85[ASN][1000 genomes]
rs9366806	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380310	0.89[ASN][1000 genomes]
rs9380311	0.87[ASN][1000 genomes]
rs9380315	0.88[ASN][1000 genomes]
rs9394102	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9394117	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9394123	0.85[EUR][1000 genomes]
rs9394154	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6899820	TMEM170B	cis	Skin Sun Exposed Lower leg	GTEx
rs6899820	TMEM170B	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11470200-11479200	Weak transcription	Fetal Kidney	kidney
2	chr6:11474000-11477200	Weak transcription	Aorta	Aorta
3	chr6:11475000-11477000	Weak transcription	Ovary	ovary
4	chr6:11475000-11480600	Weak transcription	Placenta	Placenta
5	chr6:11475600-11477200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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