Variant report

Variant	rs2299698
Chromosome Location	chr20:52666010-52666011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:59805932..59807613-chr20:52665362..52667872,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11905945	0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs12479663	1.00[LWK][hapmap]
rs1381983	0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs1381984	0.89[EUR][1000 genomes]
rs1557853	0.83[GIH][hapmap];0.88[EUR][1000 genomes]
rs2072128	0.83[GIH][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs2107327	0.91[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2189502	0.89[EUR][1000 genomes]
rs2214530	0.89[EUR][1000 genomes]
rs2238701	0.89[AMR][1000 genomes]
rs2276487	0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs2276488	0.89[EUR][1000 genomes]
rs2276489	0.89[EUR][1000 genomes]
rs2276491	0.92[EUR][1000 genomes]
rs2299699	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299701	0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs2299702	0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs2299704	0.83[JPT][hapmap]
rs2299705	0.89[EUR][1000 genomes]
rs2299707	0.89[EUR][1000 genomes]
rs2299711	0.88[EUR][1000 genomes]
rs2299712	0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2299715	0.92[EUR][1000 genomes]
rs2299718	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2870304	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]
rs34973146	0.89[EUR][1000 genomes]
rs35883829	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6091807	0.91[EUR][1000 genomes]
rs6091811	0.89[EUR][1000 genomes]
rs6091812	0.89[EUR][1000 genomes]
rs6097745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6097749	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6123345	0.92[EUR][1000 genomes]
rs6127058	0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs6127060	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6127061	0.91[EUR][1000 genomes]
rs6127062	0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6127063	0.92[EUR][1000 genomes]
rs6127065	0.89[EUR][1000 genomes]
rs6127066	0.88[EUR][1000 genomes]
rs6127068	0.89[EUR][1000 genomes]
rs6127072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67082409	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71323984	0.93[EUR][1000 genomes]
rs73133436	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs732344	0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs765348	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
3	esv2763673	chr20:52637074-52668126	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv3419	chr20:52637581-52672115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
5	nsv1055891	chr20:52647808-52666885	Enhancers Strong transcription Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv1067336	chr20:52647808-52668126	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv1065888	chr20:52647808-52670378	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv586250	chr20:52647823-52671132	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv1055306	chr20:52651154-52666885	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299698	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	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:52665400-52666400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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