Variant report

Variant	rs12440292
Chromosome Location	chr15:59884098-59884099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10083653	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10163153	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11852448	0.86[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11852458	0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs12438840	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12902622	0.88[CEU][hapmap];0.93[MEX][hapmap];0.81[EUR][1000 genomes]
rs1479883	0.84[ASN][1000 genomes]
rs1479884	0.84[ASN][1000 genomes]
rs1552033	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1552034	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1600406	0.83[ASN][1000 genomes]
rs17236671	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17269684	0.88[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28514722	0.81[EUR][1000 genomes]
rs28634844	0.83[ASN][1000 genomes]
rs34444281	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34526393	0.84[ASN][1000 genomes]
rs34642067	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35046363	0.88[ASN][1000 genomes]
rs35208294	0.88[ASN][1000 genomes]
rs35461856	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35743616	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4597252	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67189240	0.92[ASN][1000 genomes]
rs71480534	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71480535	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71480536	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7169937	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7171752	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8036403	0.81[GIH][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8037054	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv569606	chr15:59883809-59894636	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12440292	TCF12	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59882400-59884200	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:59882400-59891600	Weak transcription	Small Intestine	intestine
3	chr15:59882600-59884200	Enhancers	GM12878-XiMat	blood
4	chr15:59883000-59884200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr15:59883000-59884400	Enhancers	Duodenum Mucosa	Duodenum
6	chr15:59883200-59884200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:59883200-59884200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr15:59883200-59884200	Enhancers	Fetal Intestine Small	intestine
9	chr15:59883200-59884200	Enhancers	Stomach Mucosa	stomach
10	chr15:59883200-59884400	Enhancers	Fetal Intestine Large	intestine
11	chr15:59883200-59884600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr15:59883200-59884600	Enhancers	NHEK	skin
13	chr15:59883400-59884200	Enhancers	A549	lung
14	chr15:59883400-59884600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:59883600-59884200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:59883600-59884200	Enhancers	Fetal Heart	heart
17	chr15:59883600-59884400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:59883600-59884400	Enhancers	HMEC	breast
19	chr15:59883600-59887200	Weak transcription	Colonic Mucosa	Colon
20	chr15:59883800-59884200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:59883800-59884200	Enhancers	HepG2	liver
22	chr15:59883800-59887400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:59884000-59884600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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