Variant report

Variant	rs11639249
Chromosome Location	chr15:41914597-41914598
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	chr15:41913263..41914798-chr15:41951320..41953702,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10152332	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10152364	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10775122	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775123	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10775124	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11070345	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11070347	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11632100	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11634840	0.82[ASN][1000 genomes]
rs11639146	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148330	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12441249	0.84[ASN][1000 genomes]
rs12900295	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902548	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12915325	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12916525	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916992	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1867416	0.81[ASN][1000 genomes]
rs1867417	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1899819	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899820	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1899821	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2141141	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2178004	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2577954	0.81[AMR][1000 genomes]
rs4244585	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4371125	0.84[ASN][1000 genomes]
rs4465584	0.84[AMR][1000 genomes]
rs4923908	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4924568	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4924571	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4924572	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62002069	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6493008	0.84[AMR][1000 genomes]
rs6493010	0.82[AMR][1000 genomes]
rs7164209	0.84[ASN][1000 genomes]
rs7169496	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7169668	0.84[ASN][1000 genomes]
rs7176474	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177232	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177911	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7178205	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8027390	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8028886	0.81[ASN][1000 genomes]
rs8030179	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8034261	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8038783	0.84[ASN][1000 genomes]
rs8039440	0.84[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
rs11639249	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41912600-41915000	Active TSS	A549	lung
2	chr15:41912800-41914600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:41912800-41914600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr15:41912800-41914600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr15:41912800-41914600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:41912800-41914600	Flanking Active TSS	HepG2	liver
7	chr15:41912800-41914800	Active TSS	Brain Anterior Caudate	brain
8	chr15:41912800-41915000	Active TSS	Fetal Brain Female	brain
9	chr15:41913000-41914600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:41913000-41914600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr15:41913000-41914600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:41913000-41914600	Active TSS	Brain Substantia Nigra	brain
13	chr15:41913000-41914600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr15:41913000-41914600	Active TSS	Ovary	ovary
15	chr15:41913000-41914600	Active TSS	Psoas Muscle	Psoas
16	chr15:41913000-41914600	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr15:41913000-41914600	Active TSS	Rectal Smooth Muscle	rectum
18	chr15:41913000-41914600	Active TSS	Right Atrium	heart
19	chr15:41913000-41914600	Active TSS	HSMM	muscle
20	chr15:41913000-41914600	Active TSS	HSMMtube	muscle
21	chr15:41913000-41914800	Active TSS	Brain Cingulate Gyrus	brain
22	chr15:41913200-41914600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:41913200-41914600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr15:41913200-41914600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
25	chr15:41913200-41914600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr15:41913200-41914600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:41913200-41914600	Active TSS	Fetal Lung	lung
28	chr15:41913200-41914600	Flanking Active TSS	Placenta	Placenta
29	chr15:41913200-41914800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr15:41913200-41914800	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr15:41913200-41914800	Active TSS	Brain Angular Gyrus	brain
32	chr15:41913200-41915000	Active TSS	Fetal Kidney	kidney
33	chr15:41913400-41914600	Active TSS	Brain Germinal Matrix	brain
34	chr15:41913400-41914600	Active TSS	Brain Hippocampus Middle	brain
35	chr15:41913400-41914800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:41913400-41914800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:41913600-41914600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:41913600-41914600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:41913600-41914600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:41913600-41914600	Active TSS	Liver	Liver
41	chr15:41913600-41914600	Active TSS	Duodenum Mucosa	Duodenum
42	chr15:41913600-41914600	Active TSS	Dnd41	blood
43	chr15:41913600-41914600	Bivalent/Poised TSS	NHEK	skin
44	chr15:41913600-41915000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:41913800-41914600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:41913800-41914600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr15:41913800-41915000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr15:41913800-41939400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:41914000-41914600	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr15:41914000-41914600	Flanking Active TSS	Fetal Muscle Leg	muscle

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