Variant report

Variant	rs1570670
Chromosome Location	chr20:52774579-52774580
allele	A/G
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	ETS1	chr20:52773955-52775057	A549	lung:	n/a	n/a
2	SIN3AK20	chr20:52774334-52774793	A549	lung:	n/a	n/a
3	USF1	chr20:52772419-52775161	A549	lung:	n/a	n/a
4	TEAD4	chr20:52772674-52774894	A549	lung:	n/a	n/a
5	REST	chr20:52772302-52776022	A549	lung:	n/a	n/a
6	FOSL2	chr20:52772174-52775929	A549	lung:	n/a	n/a
7	TCF12	chr20:52772200-52791801	A549	lung:	n/a	chr20:52790233-52790240 chr20:52786044-52786053 chr20:52779960-52779969 chr20:52790231-52790241
8	ELF1	chr20:52774493-52774819	A549	lung:	n/a	n/a
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

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
ENSG00000196562	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1570669	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.99[ASN][1000 genomes]
rs1985565	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296237	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296240	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787553	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4809956	0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4809957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4811494	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56808842	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59895069	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6091824	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6091825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097805	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097806	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097807	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751087	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751089	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927648	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs927651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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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