Variant report

Variant	rs1353887
Chromosome Location	chr3:142700273-142700274
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142682070..142686174-chr3:142699444..142703436,4	K562	blood:
2	chr3:142682998..142686174-chr3:142699444..142703436,4	K562	blood:
3	chr3:142694373..142698058-chr3:142700090..142703022,3	K562	blood:
4	chr3:142699274..142702132-chr3:142719844..142723108,4	K562	blood:
5	chr3:142646642..142649526-chr3:142698075..142700491,2	K562	blood:
6	chr3:142699207..142701682-chr3:142709605..142712109,2	K562	blood:
7	chr3:142646363..142649526-chr3:142696686..142700491,3	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000268129	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000188582	Chromatin interaction
ENSG00000241570	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11917259	0.85[JPT][hapmap]
rs11925953	0.85[JPT][hapmap]
rs16852909	0.85[JPT][hapmap]
rs17557349	0.85[JPT][hapmap]
rs17633378	0.85[JPT][hapmap]
rs2173599	0.85[JPT][hapmap]
rs251483	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs251488	0.81[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs669354	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865584	0.87[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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1353887	CLSTN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142695800-142701000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:142695800-142701000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:142695800-142701400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:142695800-142705800	Weak transcription	Left Ventricle	heart
5	chr3:142696000-142705800	Weak transcription	Right Atrium	heart
6	chr3:142698600-142700800	Enhancers	K562	blood
7	chr3:142699000-142701600	Enhancers	A549	lung
8	chr3:142699600-142701400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:142699600-142704600	Enhancers	HepG2	liver
10	chr3:142699800-142700400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:142699800-142700600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr3:142699800-142701600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:142700000-142700400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:142700000-142701600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:142700200-142700600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:142700200-142701600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:142700200-142701600	Enhancers	HUES64 Cell Line	embryonic stem cell

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

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