Variant report

Variant	rs12635273
Chromosome Location	chr3:157203453-157203454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1011060	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1350149	0.81[CHB][hapmap]
rs2165873	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4258914	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4611770	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679796	0.88[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4680371	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs4680372	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs62280982	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441133	0.80[CHB][hapmap]
rs67118252	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779693	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682174	0.82[CHB][hapmap]
rs988757	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv32988	chr3:157200833-157209334	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12635273	VEPH1	cis	cerebellum	SCAN
rs12635273	RAD9A	trans	cerebellum	SCAN
rs12635273	C3orf55	cis	parietal	SCAN
rs12635273	KPNA4	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157185600-157211400	Weak transcription	HSMM	muscle
2	chr3:157187600-157210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:157194000-157212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:157194400-157210200	Weak transcription	NH-A	brain
5	chr3:157194600-157217000	Weak transcription	Pancreas	Pancrea
6	chr3:157194800-157212000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:157198800-157204400	Weak transcription	HUVEC	blood vessel
8	chr3:157198800-157210400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:157199000-157211600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:157200600-157203600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:157201200-157206800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:157201800-157204600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:157202400-157204000	Weak transcription	Osteobl	bone
14	chr3:157203000-157204200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:157203200-157204200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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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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