Variant report

Variant	rs6110220
Chromosome Location	chr20:14245838-14245839
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	chr20:14173827..14175153-chr20:14245201..14246183,6	MCF-7	breast:
2	chr20:14170212..14170967-chr20:14245501..14246136,3	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11087084	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs12329405	0.92[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap]
rs12624446	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1570486	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs204629	0.85[JPT][hapmap]
rs204636	0.85[JPT][hapmap]
rs204637	0.85[JPT][hapmap]
rs2145560	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs2208454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2208456	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs2327846	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2327847	0.86[ASN][1000 genomes]
rs3789335	0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs6033952	0.85[JPT][hapmap]
rs6042695	0.85[JPT][hapmap]
rs6105236	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]
rs6105243	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs6105245	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6105246	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs6105247	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs6105250	0.84[EUR][1000 genomes]
rs6110208	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6110235	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6110242	0.84[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6110247	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6110251	0.82[EUR][1000 genomes]
rs6110252	0.89[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs6110255	0.92[JPT][hapmap]
rs6110259	0.92[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap]
rs6110263	0.80[EUR][1000 genomes]
rs6110264	0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs6131564	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6135108	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135109	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135124	0.82[EUR][1000 genomes]
rs6135125	0.89[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs6135127	0.92[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs6135128	0.94[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs743216	0.89[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs8126410	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv532514	chr20:14097780-14288315	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv458872	chr20:14189779-14317390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv470540	chr20:14189779-14317390	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv585439	chr20:14189779-14317390	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1066105	chr20:14201909-14272115	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6110220	OVOL2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
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