Variant report

Variant	rs6098074
Chromosome Location	chr20:53167472-53167473
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	JUND	chr20:53167381-53167748	HepG2	liver:	n/a	chr20:53167559-53167570
2	JUND	chr20:53166955-53168040	SK-N-SH	brain:	n/a	chr20:53167559-53167570
3	FOS	chr20:53167412-53167629	MCF10A-Er-Src	breast:	n/a	chr20:53167559-53167570
4	JUN	chr20:53167419-53167689	HepG2	liver:	n/a	n/a
5	FOS	chr20:53167445-53167710	MCF10A-Er-Src	breast:	n/a	chr20:53167559-53167570
6	FOS	chr20:53167295-53167727	HUVEC	blood vessel:	n/a	chr20:53167559-53167570
7	GATA3	chr20:53166844-53168199	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:53165477..53168147-chr20:53202894..53205651,2	MCF-7	breast:
2	chr17:77787431..77788987-chr20:53166127..53168604,2	MCF-7	breast:
3	chr2:141422971..141423545-chr20:53166808..53167673,2	MCF-7	breast:
4	chr20:53158565..53163438-chr20:53165298..53171299,6	MCF-7	breast:

Variant related genes	Relation type
DOK5	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16999731	0.86[CHD][hapmap]
rs16999736	0.86[CHD][hapmap]
rs16999764	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16999772	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2426522	0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes]
rs2426529	0.85[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes]
rs2426530	0.85[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes]
rs2426536	0.82[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58686390	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6014049	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6014050	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6014052	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6014053	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6014055	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6014056	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6014057	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6014058	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6023344	0.87[AMR][1000 genomes]
rs6023357	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6023362	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6091909	0.85[CHD][hapmap]
rs6098064	0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62214421	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214425	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs726770	0.85[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes]
rs7272302	0.85[CEU][hapmap]
rs7274532	0.85[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8117905	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8126261	0.86[CHD][hapmap];0.84[MEX][hapmap]
rs974461	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9917433	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[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:9 , 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	chr20:53164000-53167800	Enhancers	Fetal Brain Female	brain
4	chr20:53165200-53168400	Enhancers	Fetal Brain Male	brain
5	chr20:53165800-53167800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:53166000-53167800	Enhancers	Osteobl	bone
7	chr20:53166400-53177400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr20:53166800-53173600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:53166800-53176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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