Variant report

Variant	rs12915990
Chromosome Location	chr15:78467777-78467778
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:78467775-78467837	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ACSBG1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11072738	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11855354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12903696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1982242	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304824	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495275	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495276	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7172176	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8032618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034946	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920103	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs9972613	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS 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	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12915990	IDH3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78449000-78467800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:78457000-78468400	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:78458800-78468800	Weak transcription	Stomach Mucosa	stomach
5	chr15:78459000-78470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:78460200-78474200	Weak transcription	HepG2	liver
7	chr15:78461800-78471000	Weak transcription	Psoas Muscle	Psoas
8	chr15:78462000-78468000	Strong transcription	Gastric	stomach
9	chr15:78463000-78468200	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:78464600-78468000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:78464600-78469800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:78464800-78467800	Weak transcription	Colonic Mucosa	Colon
13	chr15:78464800-78468400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:78464800-78468800	Enhancers	Primary hematopoietic stem cells	blood
15	chr15:78464800-78470000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:78464800-78475000	Weak transcription	HMEC	breast
17	chr15:78465000-78468800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:78465000-78469800	Weak transcription	Hela-S3	cervix
19	chr15:78465000-78470000	Weak transcription	HSMM	muscle
20	chr15:78465200-78467800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:78465200-78467800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:78465200-78467800	Weak transcription	Osteobl	bone
23	chr15:78465200-78468200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:78465200-78468800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:78465200-78469600	Weak transcription	Right Ventricle	heart
26	chr15:78465200-78469800	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:78465200-78474200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:78465200-78475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:78465200-78475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:78465400-78467800	Weak transcription	Fetal Lung	lung
31	chr15:78465400-78468000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:78465400-78468200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:78465400-78470000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:78465400-78470000	Weak transcription	Placenta	Placenta
35	chr15:78465400-78474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:78465400-78475200	Weak transcription	NHEK	skin
37	chr15:78465800-78467800	Flanking Active TSS	Thymus	Thymus
38	chr15:78466000-78468000	Weak transcription	Lung	lung
39	chr15:78466000-78468000	Flanking Active TSS	Dnd41	blood
40	chr15:78466000-78469800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:78466000-78469800	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:78466000-78470000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:78466200-78468800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr15:78466200-78469200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:78466200-78470000	Weak transcription	Left Ventricle	heart
46	chr15:78466400-78467800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr15:78466400-78468000	Weak transcription	Adipose Nuclei	Adipose
48	chr15:78466400-78470200	Weak transcription	A549	lung
49	chr15:78466600-78468400	Weak transcription	Pancreas	Pancrea
50	chr15:78466800-78468000	Enhancers	GM12878-XiMat	blood

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