Variant report

Variant	rs12913189
Chromosome Location	chr15:92565607-92565608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12593984	0.83[JPT][hapmap]
rs12899498	0.80[AMR][1000 genomes]
rs12899673	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904266	0.83[JPT][hapmap]
rs12905838	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12905905	0.93[CHB][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs12905912	0.83[JPT][hapmap]
rs12906289	0.93[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12912272	0.81[JPT][hapmap]
rs12912997	0.83[JPT][hapmap]
rs35000646	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57842850	0.94[ASN][1000 genomes]
rs62011580	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71411125	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7163548	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7166185	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7178378	0.83[JPT][hapmap]
rs7181178	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8040010	0.83[JPT][hapmap]

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	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv984212	chr15:92562075-92570410	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12913189	ACAN	cis	parietal	SCAN
rs12913189	DET1	cis	parietal	SCAN
rs12913189	FES	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92554200-92566200	Enhancers	Right Atrium	heart
2	chr15:92555600-92570600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr15:92555600-92576200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:92557800-92567000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:92558000-92571200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:92558600-92568600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:92562000-92567800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:92562600-92570600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:92562800-92565800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:92562800-92566400	Enhancers	Adipose Nuclei	Adipose
11	chr15:92562800-92569600	Enhancers	Fetal Heart	heart
12	chr15:92562800-92574600	Weak transcription	Esophagus	oesophagus
13	chr15:92563400-92566000	Weak transcription	Left Ventricle	heart
14	chr15:92563800-92567000	Weak transcription	Brain Substantia Nigra	brain
15	chr15:92563800-92568200	Enhancers	Aorta	Aorta
16	chr15:92564000-92566200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr15:92564000-92567200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:92564400-92565800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:92564600-92570000	Enhancers	Brain Hippocampus Middle	brain
20	chr15:92564600-92571400	Weak transcription	Small Intestine	intestine
21	chr15:92564800-92566600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:92564800-92567000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:92565000-92566200	Enhancers	Brain Angular Gyrus	brain
24	chr15:92565200-92566000	Weak transcription	Lung	lung
25	chr15:92565200-92566000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:92565200-92566000	Weak transcription	Right Ventricle	heart
27	chr15:92565200-92569200	Weak transcription	Spleen	Spleen
28	chr15:92565200-92571400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:92565200-92572000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:92565200-92573400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:92565400-92565800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:92565400-92567200	Weak transcription	Brain Anterior Caudate	brain
33	chr15:92565400-92568200	Weak transcription	Ovary	ovary
34	chr15:92565400-92572400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:92565600-92566200	Enhancers	Skeletal Muscle Female	skeletal muscle

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