Variant report

Variant	rs4339862
Chromosome Location	chr1:159441628-159441629
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10797035	0.84[ASN][1000 genomes]
rs11265216	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12127080	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12564019	0.85[CHD][hapmap]
rs12566875	0.86[CHB][hapmap]
rs4128726	0.85[CHD][hapmap]
rs4233351	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4233352	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4540655	0.82[ASN][1000 genomes]
rs4656837	0.91[GIH][hapmap];0.90[JPT][hapmap]
rs6680456	0.83[ASN][1000 genomes]
rs6687518	0.83[ASN][1000 genomes]
rs7525975	0.83[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	esv3334702	chr1:159415928-159442349	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv432975	chr1:159431927-159461927	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4339862	THBS3	cis	cerebellum	SCAN
rs4339862	TMEM79	cis	cerebellum	SCAN
rs4339862	PMVK	cis	cerebellum	SCAN
rs4339862	MUC1	cis	parietal	SCAN
rs4339862	CD48	cis	cerebellum	SCAN
rs4339862	C1orf189	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159438200-159444600	Enhancers	HUVEC	blood vessel
2	chr1:159439600-159445400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:159440400-159456600	Weak transcription	Liver	Liver
4	chr1:159441600-159442600	Weak transcription	Osteobl	bone

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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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