Variant report

Variant	rs6042301
Chromosome Location	chr20:13656265-13656266
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13652495..13656691-chr20:13764074..13766067,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101247	Chromatin interaction
ENSG00000089048	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1040756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11087055	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11087056	0.96[EUR][1000 genomes]
rs13040087	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2295503	0.82[ASN][1000 genomes]
rs2295504	0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2327793	0.88[ASN][1000 genomes]
rs2423732	0.84[ASN][1000 genomes]
rs2423733	0.85[ASN][1000 genomes]
rs2423734	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2423736	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2423737	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2423738	0.88[ASN][1000 genomes]
rs2423739	0.88[ASN][1000 genomes]
rs34146992	0.81[ASN][1000 genomes]
rs34822601	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4303776	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4441543	0.90[ASN][1000 genomes]
rs6033766	0.82[ASN][1000 genomes]
rs6033767	0.84[ASN][1000 genomes]
rs6033768	0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6033783	0.84[ASN][1000 genomes]
rs6033793	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6033795	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033803	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033804	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042225	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6042236	0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6042239	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6042240	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6042264	0.82[ASN][1000 genomes]
rs6042273	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6042285	0.89[ASN][1000 genomes]
rs6042304	0.96[EUR][1000 genomes]
rs6105137	0.84[ASN][1000 genomes]
rs6109983	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6109990	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6109993	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6109995	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6131499	0.86[ASN][1000 genomes]
rs6134930	0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6134935	0.82[ASN][1000 genomes]
rs6134948	0.84[ASN][1000 genomes]
rs6514418	0.85[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13652800-13656800	Weak transcription	Fetal Stomach	stomach
2	chr20:13653000-13659000	Weak transcription	Thymus	Thymus
3	chr20:13653600-13657000	Weak transcription	Fetal Lung	lung
4	chr20:13655600-13656800	Weak transcription	Dnd41	blood

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