Variant report

Variant	rs7342408
Chromosome Location	chr12:117974728-117974729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1393076	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767557	0.90[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	nsv560386	chr12:117822187-117991547	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv832527	chr12:117974007-118110244	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv528755	chr12:117974728-117984413	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7342408	LHX5	cis	cerebellum	SCAN
rs7342408	TAOK3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117940200-117978600	Weak transcription	Brain Anterior Caudate	brain
2	chr12:117953000-117995600	Weak transcription	Brain Angular Gyrus	brain
3	chr12:117957000-117995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:117963000-117977400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:117963600-117979200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:117965200-117995800	Weak transcription	Pancreas	Pancrea
7	chr12:117970800-117981600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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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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