Variant report

Variant	rs16885209
Chromosome Location	chr6:54179040-54179041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54177292..54179184-chr6:54200767..54202415,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10085239	0.84[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12204972	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs17755505	0.83[GIH][hapmap]
rs17828521	0.83[GIH][hapmap]
rs2202801	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2297982	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2297985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736352	0.83[GIH][hapmap]
rs3736353	0.83[GIH][hapmap]
rs3777648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777656	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777660	0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3822896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41413844	0.83[GIH][hapmap]
rs57216370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58994452	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60267994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464052	0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9474797	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs9474831	0.83[GIH][hapmap]
rs949469	0.83[GIH][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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54176600-54191800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54176600-54191800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:54178200-54188400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:54178200-54191600	Weak transcription	Fetal Intestine Large	intestine
5	chr6:54179000-54179200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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