Variant report

Variant	rs2870304
Chromosome Location	chr20:52673217-52673218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52556030..52560309-chr20:52671948..52677336,4	K562	blood:
2	chr20:52673211..52674158-chr20:52814408..52815314,3	MCF-7	breast:
3	chr20:52445412..52448214-chr20:52672686..52675334,2	MCF-7	breast:
4	chr20:52671848..52674033-chr20:55841179..55843003,2	MCF-7	breast:
5	chr20:52671492..52674058-chr20:55837796..55841174,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236352	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11905945	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1381983	0.86[EUR][1000 genomes]
rs1381984	0.86[EUR][1000 genomes]
rs1557853	0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs2072128	0.91[GIH][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2107327	0.84[ASW][hapmap];0.83[GIH][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2189502	0.86[EUR][1000 genomes]
rs2214530	0.86[EUR][1000 genomes]
rs2238701	0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2276487	0.86[EUR][1000 genomes]
rs2276488	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2276489	0.86[EUR][1000 genomes]
rs2276491	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2299698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299699	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2299701	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2299702	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2299704	0.84[ASW][hapmap]
rs2299705	0.86[EUR][1000 genomes]
rs2299707	0.86[EUR][1000 genomes]
rs2299711	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2299712	0.87[GIH][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2299715	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2299718	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34973146	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35883829	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6091807	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6091811	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6091812	0.86[EUR][1000 genomes]
rs6097745	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6097749	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6123345	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6127058	0.90[EUR][1000 genomes]
rs6127060	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6127061	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6127062	0.87[GIH][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6127063	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6127065	0.86[EUR][1000 genomes]
rs6127066	0.86[EUR][1000 genomes]
rs6127068	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6127072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6127073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67082409	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71323984	0.91[EUR][1000 genomes]
rs73133436	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs732344	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2870304	ZNF185	trans	lymphoblastoid	seeQTL
rs2870304	C20orf106	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr20:52666600-52675200	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr20:52669400-52681800	Weak transcription	Gastric	stomach
5	chr20:52673000-52674000	Weak transcription	Rectal Mucosa Donor 29	rectum

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