Variant report

Variant	rs8123293
Chromosome Location	chr20:52718555-52718556
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52718236..52723040-chr20:52810797..52817780,169	MCF-7	breast:
2	chr17:56978457..56980198-chr20:52716373..52719120,2	MCF-7	breast:
3	chr17:56706304..56710637-chr20:52708902..52722942,22	MCF-7	breast:
4	chr20:52718018..52720477-chr8:101320363..101322308,2	MCF-7	breast:
5	chr20:46294406..46296720-chr20:52718393..52720596,2	MCF-7	breast:
6	chr17:57921397..57924347-chr20:52716590..52720160,4	MCF-7	breast:
7	chr20:46410730..46421216-chr20:52711028..52724253,28	MCF-7	breast:
8	chr20:52718541..52720185-chr20:52811223..52812435,5	MCF-7	breast:
9	chr20:52715909..52718774-chr20:55838311..55841163,2	MCF-7	breast:
10	chr20:52718490..52719463-chr20:52815969..52817223,5	MCF-7	breast:
11	chr20:52718555..52719158-chr20:52739812..52740855,3	MCF-7	breast:
12	chr20:52718473..52720185-chr20:52811223..52812490,9	MCF-7	breast:
13	chr17:57859882..57862542-chr20:52718438..52720258,2	MCF-7	breast:
14	chr20:52718501..52719345-chr20:52743465..52744028,2	MCF-7	breast:
15	chr17:56735120..56739266-chr20:52717504..52723217,7	MCF-7	breast:
16	chr17:56734263..56738304-chr20:52709856..52719047,15	MCF-7	breast:
17	chr17:56703018..56712407-chr20:52697460..52725685,93	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000267637	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000034677	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1477641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs1841850	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6013891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs6013892	0.89[CEU][hapmap]
rs6022964	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6097766	0.88[AMR][1000 genomes];0.84[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8123293	SPO11	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52714000-52721200	Weak transcription	HMEC	breast
2	chr20:52714000-52721800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:52715800-52719800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr20:52717800-52719200	Enhancers	A549	lung
5	chr20:52718000-52720200	Enhancers	Placenta	Placenta
6	chr20:52718400-52719800	Enhancers	HepG2	liver

Quick Search:

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

what's new

Quick links