Variant report

Variant	rs6042647
Chromosome Location	chr20:1480271-1480272
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1453675..1455747-chr20:1479938..1482254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11697322	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11699494	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163	1.00[ASN][1000 genomes]
rs16994549	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883933	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883936	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57094926	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033911	1.00[ASN][1000 genomes]
rs6033914	1.00[ASN][1000 genomes]
rs6033918	1.00[ASN][1000 genomes]
rs6033923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033936	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042588	1.00[ASN][1000 genomes]
rs6042676	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042682	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042689	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60645920	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66715055	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715217	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8117719	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1475400-1480800	Weak transcription	Fetal Thymus	thymus
2	chr20:1475600-1480800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr20:1476000-1480800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr20:1476000-1480800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr20:1476200-1481000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr20:1476200-1481400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr20:1476600-1484000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:1478800-1480800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr20:1479000-1482200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:1479600-1482200	Enhancers	HMEC	breast
11	chr20:1479800-1482200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:1480000-1481200	Flanking Active TSS	NHEK	skin
13	chr20:1480000-1481800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr20:1480000-1482000	Enhancers	Placenta	Placenta
15	chr20:1480200-1481000	Enhancers	Hela-S3	cervix
16	chr20:1480200-1481200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:1480200-1481600	Weak transcription	Esophagus	oesophagus
18	chr20:1480200-1481800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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