Variant report

Variant	rs6109534
Chromosome Location	chr20:12727209-12727210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13042602	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1831808	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1831809	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2225617	0.99[EUR][1000 genomes]
rs6041588	0.99[EUR][1000 genomes]
rs6041590	0.99[EUR][1000 genomes]
rs6041595	0.99[EUR][1000 genomes]
rs6104961	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109532	0.99[EUR][1000 genomes]
rs6109533	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109537	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73900230	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058919	chr20:11917331-12733316	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544183	chr20:11917331-12733316	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv18943	chr20:12627634-12841804	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv2763218	chr20:12717131-12728818	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv585433	chr20:12724326-12756660	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12720200-12728800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:12724000-12728000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr20:12725000-12728800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr20:12725200-12728600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr20:12725200-12728800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr20:12725600-12728600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr20:12726200-12727400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr20:12727200-12728600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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