Variant report

Variant	rs12915829
Chromosome Location	chr15:41877960-41877961
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41407897..41409667-chr15:41876461..41878858,2	MCF-7	breast:
2	chr15:41757459..41758345-chr15:41877423..41878368,2	MCF-7	breast:
3	chr15:41855197..41857577-chr15:41876968..41879367,2	K562	blood:
4	chr15:41870694..41874947-chr15:41876174..41878118,3	K562	blood:
5	chr15:41870467..41873632-chr15:41874350..41878118,3	K562	blood:
6	chr15:41848431..41851205-chr15:41877401..41879696,2	K562	blood:

Variant related genes	Relation type
ENSG00000259838	Chromatin interaction
ENSG00000092445	Chromatin interaction
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10438299	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1077714	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12906912	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2246444	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2277537	0.82[AMR][1000 genomes]
rs2482307	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28655000	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28792443	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28844285	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784283	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924552	0.83[EUR][1000 genomes]
rs4924554	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924556	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924559	0.82[ASN][1000 genomes]
rs66906913	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68058196	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166371	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183231	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8025165	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12915829	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41877000-41878200	Active TSS	Ovary	ovary
2	chr15:41877200-41878000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:41877200-41878000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:41877200-41878000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr15:41877200-41878000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:41877200-41878000	Active TSS	Rectal Smooth Muscle	rectum
7	chr15:41877200-41878000	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr15:41877200-41878200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:41877200-41878200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:41877200-41878200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
11	chr15:41877200-41878200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
12	chr15:41877200-41878200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:41877200-41878200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:41877200-41878200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:41877200-41878200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:41877200-41878200	Active TSS	Colonic Mucosa	Colon
17	chr15:41877200-41878200	Active TSS	Right Ventricle	heart
18	chr15:41877200-41878200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr15:41877200-41878200	Flanking Active TSS	HUVEC	blood vessel
20	chr15:41877200-41878200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr15:41877200-41878400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:41877200-41878400	Enhancers	Fetal Heart	heart
23	chr15:41877400-41878000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:41877400-41878000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:41877400-41878000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:41877400-41878000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:41877400-41878000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr15:41877400-41878000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:41877400-41878000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:41877400-41878000	Active TSS	Brain Anterior Caudate	brain
31	chr15:41877400-41878000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr15:41877400-41878000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:41877400-41878000	Active TSS	Brain Substantia Nigra	brain
34	chr15:41877400-41878000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr15:41877400-41878000	Active TSS	Fetal Intestine Large	intestine
36	chr15:41877400-41878000	Active TSS	Gastric	stomach
37	chr15:41877400-41878000	Active TSS	Pancreas	Pancrea
38	chr15:41877400-41878000	Active TSS	HSMMtube	muscle
39	chr15:41877400-41878200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr15:41877400-41878200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:41877400-41878200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:41877400-41878200	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr15:41877400-41878200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:41877400-41878200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr15:41877400-41878200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:41877400-41878200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
47	chr15:41877400-41878200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr15:41877400-41878200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr15:41877400-41878200	Active TSS	Aorta	Aorta
50	chr15:41877400-41878200	Flanking Active TSS	Liver	Liver

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