Variant report

Variant	rs12453139
Chromosome Location	chr17:17515891-17515892
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17255767..17258601-chr17:17515737..17518655,2	K562	blood:
2	chr17:17493364..17496787-chr17:17515536..17518702,4	MCF-7	breast:
3	chr17:17512228..17514330-chr17:17515822..17518656,2	K562	blood:

Variant related genes	Relation type
ENSG00000264666	Chromatin interaction
ENSG00000133027	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12603596	0.89[ASN][1000 genomes]
rs1809205	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646340	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4646341	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4925027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925048	0.82[CHD][hapmap]
rs56745821	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57928542	0.85[ASN][1000 genomes]
rs58023844	0.82[ASN][1000 genomes]
rs7219777	0.81[CHB][hapmap]
rs73288103	0.95[ASN][1000 genomes]
rs73288113	0.87[ASN][1000 genomes]
rs8064566	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8076452	0.87[ASN][1000 genomes]
rs8081810	0.85[ASN][1000 genomes]
rs9891282	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12453139	TOP3A	cis	parietal	SCAN
rs12453139	TEKT3	cis	cerebellum	SCAN
rs12453139	TRPV2	cis	cerebellum	SCAN
rs12453139	MPRIP	cis	parietal	SCAN
rs12453139	PLD6	cis	cerebellum	SCAN
rs12453139	AKAP10	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17509400-17517800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:17510800-17516800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:17512800-17516800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:17512800-17516800	Weak transcription	Spleen	Spleen
5	chr17:17513000-17516800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:17515000-17516200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr17:17515200-17516000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:17515200-17516000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr17:17515200-17516000	Enhancers	Lung	lung
10	chr17:17515200-17516200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr17:17515200-17516200	Enhancers	Adipose Nuclei	Adipose
12	chr17:17515200-17516200	Enhancers	Fetal Heart	heart
13	chr17:17515200-17516200	Enhancers	Fetal Stomach	stomach
14	chr17:17515200-17516400	Enhancers	HepG2	liver
15	chr17:17515200-17517200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr17:17515200-17517200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr17:17515200-17517400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr17:17515400-17516000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:17515400-17516000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:17515400-17516000	Enhancers	Left Ventricle	heart
21	chr17:17515400-17516000	Enhancers	Right Atrium	heart
22	chr17:17515400-17516000	Enhancers	HSMMtube	muscle
23	chr17:17515400-17516200	Enhancers	Fetal Muscle Leg	muscle
24	chr17:17515400-17516800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr17:17515400-17517000	Enhancers	Liver	Liver
26	chr17:17515600-17516600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:17515600-17516800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr17:17515600-17516800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr17:17515600-17516800	Weak transcription	Ovary	ovary
30	chr17:17515800-17516000	Enhancers	Right Ventricle	heart
31	chr17:17515800-17516200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr17:17515800-17516800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr17:17515800-17516800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:17515800-17516800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr17:17515800-17516800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr17:17515800-17517400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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