Variant report

Variant	rs2107327
Chromosome Location	chr20:52663409-52663410
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:56735097..56736691-chr20:52662317..52665029,2	MCF-7	breast:
2	chr17:57920665..57924197-chr20:52662636..52665586,3	MCF-7	breast:
3	chr20:52637587..52640113-chr20:52663021..52665849,2	MCF-7	breast:
4	chr17:56707748..56711068-chr20:52660176..52663748,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11905945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381984	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1557853	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072128	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2189502	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2214530	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2238701	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2276487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276488	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276489	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276491	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2299698	0.91[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2299699	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[YRI][hapmap]
rs2299705	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299707	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299711	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299712	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299715	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299718	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2870304	0.84[ASW][hapmap];0.83[GIH][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34973146	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35883829	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6091807	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6091808	0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6091811	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6091812	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6097745	0.83[JPT][hapmap]
rs6097749	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6123344	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6123345	0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6127058	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6127060	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6127061	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6127062	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]
rs6127063	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6127065	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6127066	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127068	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127072	0.83[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6127073	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]
rs67082409	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71323984	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73133436	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs732344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs765348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv912940	chr20:52646029-52663409	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv912942	chr20:52646926-52663409	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1065004	chr20:52647808-52665631	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	esv2760671	chr20:52647808-52665643	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv1055891	chr20:52647808-52666885	Enhancers Strong transcription Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv1067336	chr20:52647808-52668126	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv1065888	chr20:52647808-52670378	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
12	nsv586247	chr20:52647823-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	nsv433324	chr20:52647823-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv586248	chr20:52647823-52663783	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv586249	chr20:52647823-52664869	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
16	nsv586250	chr20:52647823-52671132	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
17	nsv586260	chr20:52647830-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
18	nsv586261	chr20:52647830-52664869	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
19	nsv586268	chr20:52648368-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1055306	chr20:52651154-52666885	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
21	nsv1067083	chr20:52651609-52665631	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2107327	C20orf106	cis	parietal	SCAN

Chromatin state (count:12 , 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	chr20:52657800-52664800	Weak transcription	HSMMtube	muscle
6	chr20:52660400-52664200	Weak transcription	Right Atrium	heart
7	chr20:52661200-52665000	Weak transcription	Osteobl	bone
8	chr20:52661600-52664800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr20:52661600-52664800	Weak transcription	NHDF-Ad	bronchial
10	chr20:52661600-52665000	Weak transcription	NHLF	lung
11	chr20:52661800-52664800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr20:52663400-52664200	Enhancers	K562	blood

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