Variant report

Variant	rs460536
Chromosome Location	chr20:52679009-52679010
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:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52573818..52574952-chr20:52679002..52679930,5	MCF-7	breast:
2	chr20:52212827..52216446-chr20:52677595..52681391,3	MCF-7	breast:
3	chr20:52676834..52679503-chr20:53266669..53268779,2	MCF-7	breast:
4	chr20:52365178..52367429-chr20:52678316..52680758,2	MCF-7	breast:
5	chr20:52678920..52679915-chr3:63978931..63979877,3	MCF-7	breast:
6	chr20:52239693..52240526-chr20:52678812..52679495,2	MCF-7	breast:
7	chr20:52659902..52660887-chr20:52678920..52680381,7	MCF-7	breast:
8	chr20:45986431..45988883-chr20:52677453..52680110,2	MCF-7	breast:
9	chr20:52679000..52679535-chr20:52692581..52693450,3	MCF-7	breast:
10	chr20:52677507..52680494-chr3:64381929..64383896,2	MCF-7	breast:
11	chr20:41005640..41008273-chr20:52676406..52679770,3	MCF-7	breast:
12	chr20:52674058..52677861-chr20:52678021..52680977,4	K562	blood:
13	chr20:52678948..52679961-chr20:53262987..53263883,4	MCF-7	breast:
14	chr20:52195073..52195979-chr20:52678957..52680236,7	MCF-7	breast:
15	chr20:52669724..52670230-chr20:52678961..52679874,2	MCF-7	breast:
16	chr20:52678982..52679558-chr20:52709556..52710359,2	MCF-7	breast:
17	chr20:52678237..52680834-chr20:52687085..52688960,2	K562	blood:
18	chr20:52678959..52679775-chr20:52815946..52816831,2	MCF-7	breast:
19	chr20:52556238..52557068-chr20:52678971..52679960,5	MCF-7	breast:
20	chr20:46750253..46752428-chr20:52678041..52680092,2	MCF-7	breast:
21	chr20:52559378..52561018-chr20:52678965..52680200,31	MCF-7	breast:
22	chr20:52190970..52191876-chr20:52678761..52679613,2	MCF-7	breast:
23	chr20:52556569..52566193-chr20:52677353..52682397,12	MCF-7	breast:
24	chr20:52559216..52560998-chr20:52678738..52679912,14	MCF-7	breast:
25	chr20:52561105..52561751-chr20:52678984..52679783,3	MCF-7	breast:
26	chr20:52678972..52680191-chr20:55818951..55820251,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236352	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11699339	0.86[CHB][hapmap]
rs1531485	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1531486	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1537439	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290440	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290447	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3787547	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3787550	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs394732	0.89[YRI][hapmap]
rs458674	0.82[AFR][1000 genomes]
rs459044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459376	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs460317	0.82[AFR][1000 genomes]
rs460470	0.83[YRI][hapmap]
rs461027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462041	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462083	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462174	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs462703	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465096	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]
rs465156	0.93[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs467267	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs467321	0.82[AFR][1000 genomes]
rs6064043	0.80[CHB][hapmap]
rs6068765	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6512935	0.80[CHB][hapmap]
rs807216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs460536	BCAS1	cis	multi-tissue	Pritchard
rs460536	BCAS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 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	chr20:52675400-52679200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr20:52675600-52679200	Weak transcription	K562	blood
8	chr20:52675600-52679600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr20:52675800-52679600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr20:52676800-52679200	Weak transcription	GM12878-XiMat	blood
11	chr20:52677200-52680000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr20:52677400-52680200	Enhancers	Stomach Mucosa	stomach
13	chr20:52677600-52679400	Enhancers	HSMM	muscle
14	chr20:52677600-52679400	Enhancers	NH-A	brain
15	chr20:52677600-52679400	Enhancers	Osteobl	bone
16	chr20:52677600-52679800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr20:52677600-52679800	Enhancers	HSMMtube	muscle
18	chr20:52677600-52679800	Enhancers	NHDF-Ad	bronchial
19	chr20:52677800-52679400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr20:52677800-52679800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr20:52677800-52679800	Enhancers	Brain Cingulate Gyrus	brain
22	chr20:52677800-52679800	Enhancers	Brain Substantia Nigra	brain
23	chr20:52677800-52680000	Enhancers	Adipose Nuclei	Adipose
24	chr20:52678000-52679800	Enhancers	Fetal Heart	heart
25	chr20:52678200-52679200	Weak transcription	Brain Anterior Caudate	brain
26	chr20:52678200-52680200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr20:52678200-52683800	Weak transcription	HMEC	breast
28	chr20:52678200-52684400	Weak transcription	Fetal Stomach	stomach
29	chr20:52678400-52683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr20:52678800-52680000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr20:52679000-52679800	Enhancers	Brain Angular Gyrus	brain
32	chr20:52679000-52679800	Enhancers	Brain Hippocampus Middle	brain
33	chr20:52679000-52679800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr20:52679000-52680000	Enhancers	A549	lung

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