Variant report

Variant	rs12449964
Chromosome Location	chr17:17544704-17544705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12602348	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12936587	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943416	0.80[CEU][hapmap]
rs12945496	0.82[CEU][hapmap]
rs62066213	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9630706	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9890064	0.81[CEU][hapmap]
rs9891340	1.00[ASN][1000 genomes]
rs9900673	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9913096	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv869118	chr17:17509896-17599850	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907751	chr17:17530554-17581184	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary artery disease or ischemic stroke	24262325	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12449964	TOM1L2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17540000-17545000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:17541000-17545400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr17:17541200-17545000	Weak transcription	Fetal Stomach	stomach
4	chr17:17541600-17545400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr17:17542400-17544800	Weak transcription	Fetal Lung	lung
6	chr17:17542400-17545000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:17543600-17544800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr17:17543600-17545000	Weak transcription	Adipose Nuclei	Adipose
9	chr17:17543800-17545000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:17543800-17545000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:17543800-17545000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr17:17543800-17545000	Weak transcription	Spleen	Spleen
13	chr17:17543800-17545400	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr17:17544600-17545200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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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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