Variant report

Variant	rs12906912
Chromosome Location	chr15:41872460-41872461
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41870467..41873632-chr15:41874350..41878118,3	K562	blood:
2	chr15:41870694..41874947-chr15:41876174..41878118,3	K562	blood:

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

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

rs_ID	r²[population]
rs10438299	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1077714	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12915829	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2246444	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2277537	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2482307	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28655000	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28792443	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28844285	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3784283	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924552	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924554	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4924556	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66906913	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68058196	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7166371	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7183231	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8025165	0.88[EUR][1000 genomes]
rs8033332	0.80[AFR][1000 genomes];0.80[EUR][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	esv3312194	chr15:41868660-41873158	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv3312195	chr15:41868660-41873158	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
rs12906912	MGA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
2	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:41852600-41877400	Weak transcription	HMEC	breast
4	chr15:41852800-41877400	Weak transcription	NHEK	skin
5	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
6	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
7	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:41861000-41877200	Weak transcription	HUVEC	blood vessel
10	chr15:41861200-41877000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:41861400-41873200	Weak transcription	K562	blood
12	chr15:41863800-41873000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:41864200-41877000	Weak transcription	Fetal Kidney	kidney
14	chr15:41865800-41877000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:41865800-41877000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:41865800-41877200	Weak transcription	NHLF	lung
17	chr15:41867600-41877200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:41867600-41877200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:41868000-41877000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:41868000-41877400	Weak transcription	Esophagus	oesophagus
21	chr15:41871000-41877200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:41871200-41872600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:41871200-41873000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:41871200-41876800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:41871200-41877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:41871200-41877000	Weak transcription	Fetal Brain Female	brain
27	chr15:41871200-41877000	Weak transcription	Spleen	Spleen
28	chr15:41871200-41877200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:41871200-41877200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:41871200-41877200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:41871200-41877200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:41871200-41877200	Weak transcription	Right Atrium	heart
33	chr15:41871200-41877400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:41871200-41877400	Weak transcription	Gastric	stomach
35	chr15:41871400-41873000	Weak transcription	Placenta	Placenta
36	chr15:41871400-41873000	Weak transcription	Dnd41	blood
37	chr15:41871400-41873400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:41871400-41873800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:41871400-41874200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:41871400-41875600	Weak transcription	Fetal Intestine Large	intestine
41	chr15:41871400-41875800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:41871400-41876800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:41871400-41876800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:41871400-41877000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:41871400-41877000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:41871400-41877000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:41871400-41877000	Weak transcription	Adipose Nuclei	Adipose
48	chr15:41871400-41877000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:41871400-41877200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:41871400-41877200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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