Variant report

Variant	rs12493083
Chromosome Location	chr3:56147139-56147140
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1352008	0.90[ASN][1000 genomes]
rs1376984	0.83[CHB][hapmap]
rs4974168	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974173	0.81[CHB][hapmap]
rs59586765	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255403	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445770	0.89[CHB][hapmap]
rs6764295	0.83[CHB][hapmap]
rs6787104	0.83[CHB][hapmap]
rs7651042	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12493083	GLYCTK	cis	cerebellum	SCAN
rs12493083	ERC2	cis	cerebellum	SCAN
rs12493083	ASB14	cis	cerebellum	SCAN
rs12493083	HESX1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56144600-56152200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:56144800-56148200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56144800-56152400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:56145000-56147200	Enhancers	Fetal Lung	lung
5	chr3:56145400-56147600	Weak transcription	Fetal Brain Male	brain
6	chr3:56146000-56149200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:56146000-56151000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:56146400-56148200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:56146600-56147600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:56146600-56147800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:56146600-56148000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:56146600-56149000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:56146800-56147200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:56147000-56147400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:56147000-56147400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:56147000-56148000	Weak transcription	Brain Germinal Matrix	brain

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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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