Variant report

Variant	rs2276499
Chromosome Location	chr20:52610443-52610444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59867134..59868670-chr20:52610022..52612203,2	MCF-7	breast:
2	chr20:52609721..52610530-chr3:64020705..64021405,2	MCF-7	breast:
3	chr20:52610211..52612057-chr3:64008640..64010883,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163636	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12479580	0.80[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap]
rs1381983	0.81[CEU][hapmap]
rs208367	0.84[JPT][hapmap]
rs208379	0.81[JPT][hapmap]
rs2276498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276507	0.90[JPT][hapmap]
rs6091803	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6123336	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6123337	0.92[ASN][1000 genomes]
rs6123338	1.00[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[ASN][1000 genomes]
rs6123339	0.92[ASN][1000 genomes]
rs6127049	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6127051	0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6127053	0.88[ASN][1000 genomes]
rs6127054	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6127055	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6127060	0.81[CEU][hapmap]
rs66737174	0.92[ASN][1000 genomes]
rs66752610	0.92[ASN][1000 genomes]
rs66896772	0.92[ASN][1000 genomes]
rs66913293	0.91[ASN][1000 genomes]
rs66935272	0.92[ASN][1000 genomes]
rs67369019	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67617961	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68120080	0.84[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2276499	C20orf106	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52581200-52610600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr20:52601400-52612400	Weak transcription	Brain Angular Gyrus	brain
4	chr20:52601400-52612400	Weak transcription	Brain Anterior Caudate	brain
5	chr20:52601800-52612400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr20:52601800-52630800	Weak transcription	Stomach Mucosa	stomach
7	chr20:52604400-52618200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr20:52606800-52610600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr20:52609800-52610800	Transcr. at gene 5' and 3'	HSMMtube	muscle
10	chr20:52610000-52612600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr20:52610400-52610600	Enhancers	Brain Substantia Nigra	brain

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