Variant report

Variant	rs13041834
Chromosome Location	chr20:52703284-52703285
allele	C/T
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:46672085..46674380-chr20:52701602..52704252,2	MCF-7	breast:
2	chr20:52703014..52703715-chr20:52712947..52713871,2	MCF-7	breast:
3	chr20:41010402..41013631-chr20:52701428..52704425,3	MCF-7	breast:
4	chr17:62229187..62231839-chr20:52701894..52704628,2	MCF-7	breast:
5	chr20:46475461..46477684-chr20:52701066..52703629,2	MCF-7	breast:
6	chr20:52703278..52704196-chr20:52740076..52740823,2	MCF-7	breast:
7	chr20:52701722..52703762-chr20:55824314..55825993,2	MCF-7	breast:
8	chr20:52702899..52703599-chr3:196642311..196642817,2	MCF-7	breast:
9	chr20:52701739..52704382-chr20:55838854..55841545,2	MCF-7	breast:
10	chr20:46412955..46417498-chr20:52699874..52705785,9	MCF-7	breast:
11	chr17:56707745..56710309-chr20:52697502..52703858,9	MCF-7	breast:
12	chr17:59710076..59712294-chr20:52701398..52703517,2	MCF-7	breast:
13	chr17:56735122..56737701-chr20:52700294..52703497,3	MCF-7	breast:
14	chr17:59939183..59941685-chr20:52702690..52704309,2	MCF-7	breast:
15	chr17:60003995..60006206-chr20:52702251..52704828,2	MCF-7	breast:
16	chr20:46412091..46416534-chr20:52700009..52706788,8	MCF-7	breast:
17	chr20:52702738..52703356-chrX:30164609..30165478,2	MCF-7	breast:
18	chr17:56734710..56738015-chr20:52703039..52706122,4	MCF-7	breast:
19	chr17:56703018..56712407-chr20:52697460..52725685,93	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000108506	Chromatin interaction
ENSG00000196562	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1543703	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6064045	0.89[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6068773	0.83[AMR][1000 genomes]
rs6068774	0.82[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes]
rs6068776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs13041834	BCAS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52699200-52707000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr20:52700800-52703800	Enhancers	Stomach Mucosa	stomach
3	chr20:52701000-52706600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr20:52701800-52703800	Enhancers	Adipose Nuclei	Adipose
5	chr20:52702000-52703800	Enhancers	A549	lung
6	chr20:52702200-52707600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:52702400-52703400	Enhancers	Gastric	stomach
8	chr20:52702600-52703400	Bivalent Enhancer	HepG2	liver
9	chr20:52702600-52704400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr20:52702800-52703400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr20:52702800-52703400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr20:52702800-52703800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:52702800-52704200	Flanking Active TSS	HSMMtube	muscle
14	chr20:52702800-52704400	Enhancers	Fetal Muscle Leg	muscle
15	chr20:52703000-52703400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr20:52703000-52703800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:52703000-52703800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr20:52703000-52703800	Flanking Active TSS	Osteobl	bone
19	chr20:52703000-52704000	Flanking Active TSS	HSMM	muscle
20	chr20:52703000-52704200	Enhancers	Fetal Muscle Trunk	muscle
21	chr20:52703200-52703400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr20:52703200-52703600	Active TSS	Colonic Mucosa	Colon
23	chr20:52703200-52703800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:52703200-52703800	Active TSS	NHDF-Ad	bronchial

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