Variant report

Variant	rs12912695
Chromosome Location	chr15:78460593-78460594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78447884..78449517-chr15:78460468..78462889,2	K562	blood:
2	chr15:78438626..78440576-chr15:78459614..78461953,2	K562	blood:
3	chr15:78437651..78440580-chr15:78459542..78461046,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11629561	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630776	0.84[ASN][1000 genomes]
rs11631100	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11631653	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11634325	0.84[ASN][1000 genomes]
rs11638547	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11638921	0.87[EUR][1000 genomes]
rs12904404	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12904688	0.84[ASN][1000 genomes]
rs12904700	0.87[EUR][1000 genomes]
rs12906189	0.84[ASN][1000 genomes]
rs12910386	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12911405	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915634	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1982241	0.86[EUR][1000 genomes]
rs2044098	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2304825	0.88[EUR][1000 genomes]
rs2868607	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3816253	0.87[EUR][1000 genomes]
rs8035724	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12912695	IDH3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78442800-78463400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:78442800-78465600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:78445800-78464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:78446600-78465200	Strong transcription	Fetal Intestine Large	intestine
5	chr15:78446800-78466000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:78447600-78464400	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr15:78448000-78463000	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:78448000-78464200	Strong transcription	Liver	Liver
10	chr15:78448000-78465200	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr15:78448000-78465800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:78448400-78461000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr15:78448400-78461000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:78448600-78465400	Strong transcription	Placenta	Placenta
15	chr15:78448800-78463000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:78448800-78464200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:78448800-78466600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:78449000-78467800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:78449400-78465200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr15:78449800-78465400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:78450000-78464600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:78450000-78465200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:78450000-78465200	Strong transcription	Osteobl	bone
24	chr15:78450000-78466200	Strong transcription	Left Ventricle	heart
25	chr15:78450200-78462800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:78450200-78464200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:78450200-78465200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:78450200-78465400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:78450200-78465400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:78450600-78465200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:78451000-78464400	Strong transcription	Adipose Nuclei	Adipose
32	chr15:78451000-78466200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:78451200-78467000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr15:78451200-78467600	Strong transcription	Brain Cingulate Gyrus	brain
35	chr15:78451400-78464400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:78451400-78467200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:78451800-78462800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:78452200-78467400	Strong transcription	Brain Angular Gyrus	brain
39	chr15:78452200-78467400	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr15:78453200-78461600	Strong transcription	A549	lung
41	chr15:78453400-78465200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:78453600-78464600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:78453600-78464600	Strong transcription	Colon Smooth Muscle	Colon
44	chr15:78453600-78467400	Strong transcription	Fetal Brain Female	brain
45	chr15:78454600-78467400	Strong transcription	Brain Substantia Nigra	brain
46	chr15:78454800-78465600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr15:78455400-78462000	Weak transcription	Esophagus	oesophagus
48	chr15:78455600-78461800	Strong transcription	NH-A	brain
49	chr15:78455600-78463000	Strong transcription	Brain Anterior Caudate	brain
50	chr15:78455600-78465000	Strong transcription	HSMM	muscle

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