Variant report

Variant	rs62214503
Chromosome Location	chr20:52756201-52756202
allele	G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52749967..52752847-chr20:52755293..52758111,2	K562	blood:
2	chr17:58164161..58167016-chr20:52755740..52758316,2	MCF-7	breast:
3	chr20:49411069..49411790-chr20:52755776..52756280,2	MCF-7	breast:
4	chr20:52742787..52744481-chr20:52754993..52756803,2	K562	blood:
5	chr20:52755748..52756340-chr20:52777356..52778006,2	MCF-7	breast:
6	chr17:56735164..56738216-chr20:52753477..52757342,3	MCF-7	breast:
7	chr20:52755942..52756876-chr20:52811682..52812184,2	MCF-7	breast:
8	chr1:185122925..185124653-chr20:52755101..52757157,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12624824	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2045844	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6022979	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6091821	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6091822	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097777	0.95[ASN][1000 genomes]
rs6097779	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6097789	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097795	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097809	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6123360	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6127114	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62214478	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62214479	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8117026	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8120563	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8124440	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8124792	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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
2	nsv586280	chr20:52718555-52758416	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	84 gene(s)	inside rSNPs	diseases
3	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62214503	BCAS1	cis	inferior olivary nucleus	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52750200-52756600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:52751000-52756600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr20:52751200-52758000	Weak transcription	Placenta	Placenta
4	chr20:52751400-52757000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:52751400-52757200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr20:52751400-52758200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr20:52754000-52758400	Enhancers	HepG2	liver
8	chr20:52755600-52757000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:52755600-52758400	Enhancers	NHEK	skin
10	chr20:52755600-52758600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:52755600-52758600	Enhancers	NH-A	brain
12	chr20:52755600-52758800	Enhancers	HMEC	breast
13	chr20:52755600-52759000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:52755800-52758200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr20:52756000-52757000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:52756000-52758600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:52756200-52757400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:52756200-52758000	Enhancers	A549	lung
19	chr20:52756200-52758200	Enhancers	HSMM	muscle

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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