Variant report

Variant	rs690625
Chromosome Location	chr15:53977007-53977008
allele	C/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	FOXA2	chr15:53976442-53977238	A549	lung:	n/a	n/a
2	RXRA	chr15:53976876-53977076	HepG2	liver:	n/a	n/a
3	SP1	chr15:53976855-53977119	HepG2	liver:	n/a	n/a
4	ZBTB33	chr15:53976864-53977110	HepG2	liver:	n/a	n/a
5	POLR2A	chr15:53976900-53977056	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:53976892-53977119	H1-hESC	embryonic stem cell:	n/a	n/a
7	REST	chr15:53976884-53977021	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXA2	chr15:53976578-53977127	A549	lung:	n/a	n/a

Variant related genes	Relation type
WDR72	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10083695	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595408	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1316714	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1461410	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1461411	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1585499	0.81[EUR][1000 genomes]
rs17631603	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982601	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061600	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2459379	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2459380	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2470069	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2614204	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2614205	0.89[EUR][1000 genomes]
rs2675336	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4611400	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs474461	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475377	0.83[EUR][1000 genomes]
rs4774672	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774673	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478008	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs551225	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs552960	0.90[EUR][1000 genomes]
rs556217	0.89[EUR][1000 genomes]
rs578595	0.82[ASN][1000 genomes]
rs6416452	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493637	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493640	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493642	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs689751	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690054	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs690214	0.83[EUR][1000 genomes]
rs690383	0.90[EUR][1000 genomes]
rs690526	0.82[EUR][1000 genomes]
rs8037023	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8038719	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv9267	chr15:53821005-54132612	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv934282	chr15:53872148-53989432	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv527474	chr15:53874591-53991833	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv833010	chr15:53935652-54099849	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv569445	chr15:53974567-53985450	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53959600-53986200	Weak transcription	Pancreas	Pancrea
2	chr15:53973600-53983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:53975600-53982600	Weak transcription	Liver	Liver
4	chr15:53976000-53977200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:53976600-53990600	Weak transcription	A549	lung
6	chr15:53976800-53977200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:53977000-53977200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
8	chr15:53977000-53977200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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