Variant report

Variant	rs16999764
Chromosome Location	chr20:53170796-53170797
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	chr20:53158565..53163438-chr20:53165298..53171299,6	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs16999731	0.86[CHD][hapmap]
rs16999736	0.86[CHD][hapmap]
rs16999772	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs2426522	0.81[CHD][hapmap];0.85[TSI][hapmap]
rs2426529	0.82[CEU][hapmap]
rs2426530	0.82[CEU][hapmap]
rs2426536	0.90[CHD][hapmap]
rs58686390	0.86[ASN][1000 genomes]
rs6014049	0.90[ASN][1000 genomes]
rs6014050	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6014052	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs6014053	0.90[ASN][1000 genomes]
rs6014055	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs6014056	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs6014057	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs6014058	0.86[ASN][1000 genomes]
rs6014059	0.83[TSI][hapmap]
rs6023357	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.94[ASN][1000 genomes]
rs6023362	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6091909	0.85[CHD][hapmap]
rs6098064	0.85[CHD][hapmap]
rs6098074	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62214421	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62214425	0.86[ASN][1000 genomes]
rs726770	0.82[CEU][hapmap]
rs7272302	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7274532	0.82[CEU][hapmap];0.86[CHD][hapmap]
rs8117905	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8126261	0.86[CHD][hapmap]
rs9917433	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53162200-53172600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr20:53162400-53171600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:53166400-53177400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr20:53166800-53173600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr20:53166800-53176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:53167800-53171000	Weak transcription	Fetal Brain Female	brain
7	chr20:53167800-53174000	Weak transcription	Osteobl	bone
8	chr20:53167800-53189200	Weak transcription	Aorta	Aorta

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