Variant report

Variant	rs465096
Chromosome Location	chr20:52677705-52677706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52212827..52216446-chr20:52677595..52681391,3	MCF-7	breast:
2	chr20:52676834..52679503-chr20:53266669..53268779,2	MCF-7	breast:
3	chr20:45986431..45988883-chr20:52677453..52680110,2	MCF-7	breast:
4	chr20:52677507..52680494-chr3:64381929..64383896,2	MCF-7	breast:
5	chr20:41005640..41008273-chr20:52676406..52679770,3	MCF-7	breast:
6	chr20:52674058..52677861-chr20:52678021..52680977,4	K562	blood:
7	chr20:52675939..52678149-chr20:53262263..53264864,2	MCF-7	breast:
8	chr17:59488569..59490158-chr20:52676107..52678270,2	MCF-7	breast:
9	chr20:52677427..52678007-chr8:43092430..43093430,2	MCF-7	breast:
10	chr20:52556569..52566193-chr20:52677353..52682397,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236352	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11699339	0.90[CHB][hapmap]
rs1531485	0.89[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1531486	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1537439	0.89[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs290440	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs290447	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3787547	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3787550	0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs394732	0.89[YRI][hapmap]
rs458674	0.82[AFR][1000 genomes]
rs459044	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs459376	0.93[CEU][hapmap];0.90[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs460317	0.82[AFR][1000 genomes]
rs460470	0.83[YRI][hapmap]
rs460536	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461027	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs462041	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs462083	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs462174	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs462703	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs465156	0.90[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs467267	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs467321	0.82[AFR][1000 genomes]
rs6064043	0.85[CHB][hapmap]
rs6068765	0.89[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6068774	0.85[CHB][hapmap]
rs6512935	0.85[CHB][hapmap]
rs807216	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs465096	BCAS1	cis	multi-tissue	Pritchard
rs465096	BCAS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:52669400-52681800	Weak transcription	Gastric	stomach
3	chr20:52674400-52681200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52674400-52682000	Weak transcription	Colonic Mucosa	Colon
5	chr20:52675000-52683000	Weak transcription	HepG2	liver
6	chr20:52675200-52678800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:52675400-52679200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:52675600-52679200	Weak transcription	K562	blood
9	chr20:52675600-52679600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr20:52675800-52679600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr20:52676800-52677800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr20:52676800-52678000	Weak transcription	A549	lung
13	chr20:52676800-52679200	Weak transcription	GM12878-XiMat	blood
14	chr20:52677200-52680000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr20:52677400-52677800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:52677400-52680200	Enhancers	Stomach Mucosa	stomach
17	chr20:52677600-52678200	Enhancers	Fetal Stomach	stomach
18	chr20:52677600-52678600	Enhancers	NHEK	skin
19	chr20:52677600-52678800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr20:52677600-52678800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr20:52677600-52679400	Enhancers	HSMM	muscle
22	chr20:52677600-52679400	Enhancers	NH-A	brain
23	chr20:52677600-52679400	Enhancers	Osteobl	bone
24	chr20:52677600-52679800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:52677600-52679800	Enhancers	HSMMtube	muscle
26	chr20:52677600-52679800	Enhancers	NHDF-Ad	bronchial

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