Variant report

Variant	rs6127073
Chromosome Location	chr20:52671273-52671274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:56735085..56736750-chr20:52671034..52672707,2	MCF-7	breast:
2	chr20:52638922..52641694-chr20:52671102..52673075,2	MCF-7	breast:
3	chr17:56707459..56709744-chr20:52669878..52671451,2	MCF-7	breast:
4	chr17:56736044..56738825-chr20:52668683..52672447,3	MCF-7	breast:
5	chr17:56708938..56711128-chr20:52668141..52671621,3	MCF-7	breast:
6	chr20:52666267..52667791-chr20:52670697..52672738,2	K562	blood:

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11905945	0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1381983	0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1381984	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1557853	0.91[GIH][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2072128	0.91[GIH][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2107327	0.84[ASW][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2189502	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2214530	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276487	0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276488	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276489	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276491	0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2299698	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]
rs2299699	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299701	0.82[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2299702	0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2299704	0.84[ASW][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap]
rs2299705	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2299707	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2299711	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2299712	0.87[GIH][hapmap];0.87[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2299715	0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2299718	0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2870304	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]
rs34973146	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35883829	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6091807	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6091808	0.82[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6091811	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6091812	0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6097745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6097749	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6123344	0.81[YRI][hapmap]
rs6123345	1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6127058	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6127060	0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6127061	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6127062	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]
rs6127063	1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6127065	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6127066	0.87[EUR][1000 genomes]
rs6127068	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6127072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67082409	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71323984	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73133436	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs732344	0.83[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs765348	0.83[JPT][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6127073	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	chr20:52666400-52673000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52666600-52675200	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr20:52669400-52681800	Weak transcription	Gastric	stomach

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