Variant report

Variant	rs6127062
Chromosome Location	chr20:52636755-52636756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52636698..52639265-chr20:52824391..52826497,2	MCF-7	breast:
2	chr17:69373468..69375354-chr20:52636085..52637962,2	MCF-7	breast:
3	chr20:52628739..52630363-chr20:52636022..52638678,2	K562	blood:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11905945	1.00[CEU][hapmap];0.84[CHD][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1381983	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1381984	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1557853	1.00[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2072128	1.00[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2107327	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2189502	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2214530	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2238701	0.80[AMR][1000 genomes]
rs2276487	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276488	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276489	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299698	0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2299699	0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2299701	1.00[CEU][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299702	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299704	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs2299705	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299707	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299711	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2299712	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2299715	1.00[CEU][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2299717	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299718	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2870304	0.87[GIH][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34973146	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35883829	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3819585	0.93[ASN][1000 genomes]
rs6091807	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6091808	0.88[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6091811	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6091812	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6097749	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6123344	0.81[YRI][hapmap]
rs6123345	0.81[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127058	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127061	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127065	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6127066	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6127068	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6127072	0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6127073	0.87[GIH][hapmap];0.82[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67082409	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71323984	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73133436	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs732344	1.00[CEU][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs765348	0.85[YRI][hapmap];0.81[EUR][1000 genomes];0.81[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
rs6127062	C20orf106	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52631400-52637000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr20:52631400-52641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr20:52633800-52636800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:52633800-52638600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:52633800-52641200	Weak transcription	Brain Angular Gyrus	brain
8	chr20:52634000-52638600	Weak transcription	Brain Anterior Caudate	brain
9	chr20:52634800-52645400	Weak transcription	Fetal Lung	lung
10	chr20:52635000-52637200	Weak transcription	Brain Hippocampus Middle	brain
11	chr20:52635800-52641800	Enhancers	Brain Substantia Nigra	brain
12	chr20:52636000-52641200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr20:52636400-52636800	Weak transcription	GM12878-XiMat	blood
14	chr20:52636400-52637200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr20:52636600-52640600	Weak transcription	Stomach Mucosa	stomach

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