Variant report

Variant	rs12552179
Chromosome Location	chr9:110649490-110649491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10115778	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10816583	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10979080	0.87[ASN][1000 genomes]
rs10979081	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10979086	0.84[ASN][1000 genomes]
rs13298965	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4509400	0.84[ASN][1000 genomes]
rs7021395	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7035211	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7036874	0.88[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs7037236	0.85[ASN][1000 genomes]
rs7045461	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs944472	0.94[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051101	chr9:110548257-110697253	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12552179	OR13C2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110635800-110656800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:110644400-110651000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:110644800-110658800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:110646200-110651000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:110646400-110651000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:110646800-110652600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:110649000-110649600	Enhancers	Brain Anterior Caudate	brain
8	chr9:110649000-110649800	Enhancers	Adipose Nuclei	Adipose
9	chr9:110649200-110651000	Weak transcription	Right Atrium	heart
10	chr9:110649200-110657000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:110649400-110651000	Weak transcription	Ovary	ovary

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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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