Variant report

Variant	rs1977297
Chromosome Location	chr20:52774479-52774480
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	SIX5	chr20:52772225-52774562	A549	lung:	n/a	n/a
2	ETS1	chr20:52773955-52775057	A549	lung:	n/a	n/a
3	SIN3AK20	chr20:52774334-52774793	A549	lung:	n/a	n/a
4	USF1	chr20:52772419-52775161	A549	lung:	n/a	n/a
5	TEAD4	chr20:52772674-52774894	A549	lung:	n/a	n/a
6	REST	chr20:52772302-52776022	A549	lung:	n/a	n/a
7	FOSL2	chr20:52772174-52775929	A549	lung:	n/a	n/a
8	TCF12	chr20:52772200-52791801	A549	lung:	n/a	chr20:52790233-52790240 chr20:52786044-52786053 chr20:52779960-52779969 chr20:52790231-52790241
9	POLR2A	chr20:52770188-52790693	A549	lung:	n/a	n/a
10	BCL3	chr20:52772170-52791941	A549	lung:	n/a	chr20:52790491-52790504 chr20:52782584-52782593 chr20:52784755-52784763 chr20:52790858-52790871 chr20:52790857-52790870 chr20:52782583-52782592
11	SIN3AK20	chr20:52774146-52774705	A549	lung:	n/a	n/a
12	JUND	chr20:52772711-52775784	A549	lung:	n/a	n/a
13	ZBTB33	chr20:52774206-52774984	A549	lung:	n/a	n/a
14	BCL3	chr20:52772378-52774672	A549	lung:	n/a	n/a
15	REST	chr20:52774219-52775106	A549	lung:	n/a	n/a
16	EP300	chr20:52772794-52775025	A549	lung:	n/a	n/a
17	GATA3	chr20:52772671-52775920	A549	lung:	n/a	chr20:52775222-52775230
18	ATF3	chr20:52772261-52775274	A549	lung:	n/a	n/a
19	SP1	chr20:52773468-52774537	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:46413154..46416038-chr20:52772786..52775009,2	MCF-7	breast:
2	chr20:52697485..52699948-chr20:52774377..52776351,2	K562	blood:
3	chr17:56707553..56710474-chr20:52772691..52776017,4	MCF-7	breast:

Variant related genes	Relation type
CYP24A1	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000196562	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11905401	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11906715	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11907046	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11907150	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11907800	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11907836	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16999008	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1870967	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1886308	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2274131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4809955	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4811492	0.88[ASN][1000 genomes]
rs4811493	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55733210	0.97[ASN][1000 genomes]
rs56353101	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57016987	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57562389	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57623780	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57865579	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58978141	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59078348	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59684245	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60250398	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6091819	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6091820	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097780	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6097782	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6097783	0.97[ASN][1000 genomes]
rs6097784	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097785	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097790	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097791	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097792	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097793	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097794	0.97[ASN][1000 genomes]
rs6097796	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6097797	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6097801	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214481	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs66870448	0.98[ASN][1000 genomes]
rs7263855	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs751090	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8114002	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8114105	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8117971	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8118066	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8118441	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs873216	0.83[AMR][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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1063981	chr20:52765317-52776613	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2762085	chr20:52765329-52776625	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1058882	chr20:52765979-52794372	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52768800-52790200	Transcr. at gene 5' and 3'	A549	lung
2	chr20:52769200-52789400	Weak transcription	Esophagus	oesophagus
3	chr20:52769600-52785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52769800-52777600	Weak transcription	HepG2	liver
5	chr20:52771200-52779000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:52771200-52786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:52773400-52774800	Weak transcription	Brain Germinal Matrix	brain

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