Variant report

Variant	rs12115450
Chromosome Location	chr9:26525312-26525313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12338089	0.88[EUR][1000 genomes]
rs17754132	0.82[AFR][1000 genomes]
rs62544069	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544373	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544375	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62544378	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62544418	0.86[AFR][1000 genomes]
rs62544423	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62544457	0.94[EUR][1000 genomes]
rs62544458	0.94[EUR][1000 genomes]
rs62544459	0.94[EUR][1000 genomes]
rs62546660	0.94[EUR][1000 genomes]
rs62546661	0.94[EUR][1000 genomes]
rs7856635	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7861196	0.94[EUR][1000 genomes]
rs7874407	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995049	chr9:26162115-26760535	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv892854	chr9:26326100-26749094	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv892855	chr9:26333942-26546080	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
4	nsv1022674	chr9:26453723-26668102	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1020439	chr9:26453723-26669855	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1022289	chr9:26453723-26670583	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1029668	chr9:26486471-26531692	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12115450	TUSC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26522800-26526400	Enhancers	Fetal Stomach	stomach
2	chr9:26523000-26525400	Enhancers	Colon Smooth Muscle	Colon
3	chr9:26523200-26525400	Enhancers	Rectal Smooth Muscle	rectum
4	chr9:26523600-26525400	Enhancers	Fetal Muscle Leg	muscle
5	chr9:26523600-26525800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:26523600-26526000	Enhancers	Fetal Lung	lung
7	chr9:26524200-26525600	Enhancers	Fetal Brain Male	brain
8	chr9:26524600-26525400	Enhancers	Stomach Smooth Muscle	stomach

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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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