Variant report

Variant	rs28556632
Chromosome Location	chr15:41989730-41989731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41950960..41953076-chr15:41988289..41990930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

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

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

rs_ID	r²[population]
rs1107858	0.85[ASN][1000 genomes]
rs11634956	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637341	0.93[ASN][1000 genomes]
rs12440747	0.81[ASN][1000 genomes]
rs16952372	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16971976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677199	0.93[ASN][1000 genomes]
rs17677991	0.81[ASN][1000 genomes]
rs17678138	0.81[ASN][1000 genomes]
rs2004162	0.93[ASN][1000 genomes]
rs2412622	0.92[ASN][1000 genomes]
rs2577960	0.82[ASN][1000 genomes]
rs28700954	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28810086	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28850384	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924570	0.93[ASN][1000 genomes]
rs62002066	0.93[ASN][1000 genomes]
rs62003900	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171123	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8035855	0.88[EUR][1000 genomes];0.81[ASN][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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28556632	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
2	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:41962000-41990800	Weak transcription	NH-A	brain
4	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:41962000-42001400	Weak transcription	Gastric	stomach
6	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
10	chr15:41978800-41991200	Weak transcription	Liver	Liver
11	chr15:41981600-41995800	Weak transcription	Fetal Stomach	stomach
12	chr15:41983000-42001200	Weak transcription	Ovary	ovary
13	chr15:41983200-42002600	Weak transcription	Small Intestine	intestine
14	chr15:41984200-41990600	Weak transcription	Fetal Intestine Large	intestine
15	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:41984400-42002800	Weak transcription	A549	lung
17	chr15:41984600-41991000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:41984600-41993000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:41984600-41999200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:41984600-41999400	Weak transcription	Thymus	Thymus
21	chr15:41984600-41999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:41984600-42000600	Weak transcription	Lung	lung
23	chr15:41984600-42001600	Weak transcription	Pancreas	Pancrea
24	chr15:41984800-41991800	Weak transcription	Spleen	Spleen
25	chr15:41984800-41998800	Weak transcription	Left Ventricle	heart
26	chr15:41984800-41999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:41984800-42000800	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:41984800-42001200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:41984800-42001400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:41984800-42003000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:41985200-41996000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:41985600-41990800	Weak transcription	HSMM	muscle
33	chr15:41986000-41990600	Weak transcription	NHEK	skin
34	chr15:41987200-41990000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr15:41987600-42001200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:41988200-41990800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:41988200-41991400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:41988200-41995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:41988400-41989800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:41988400-41989800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:41988600-41989800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:41988600-42001200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:41988600-42003000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:41988600-42003000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:41988800-41989800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:41988800-41990000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:41988800-41990800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:41988800-41991200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr15:41988800-41994600	Strong transcription	Fetal Thymus	thymus
50	chr15:41988800-42002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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