Variant report

Variant	rs28700954
Chromosome Location	chr15:41953113-41953114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41850304..41852496-chr15:41951450..41954168,2	MCF-7	breast:
2	chr15:41694405..41696232-chr15:41951783..41954163,3	K562	blood:
3	chr15:41951205..41953153-chr15:41959461..41961905,2	MCF-7	breast:
4	chr15:41952932..41955703-chr15:42081114..42083481,2	K562	blood:
5	chr15:41849370..41852913-chr15:41951069..41953769,6	K562	blood:
6	chr15:41847317..41853712-chr15:41951201..41955578,8	K562	blood:
7	chr15:41952827..41953415-chr5:673974..674640,2	Hela-S3	cervix:
8	chr15:41952492..41953307-chr2:204103676..204104253,2	Hela-S3	cervix:
9	chr15:41856836..41858542-chr15:41952173..41953837,2	K562	blood:
10	chr15:41952550..41954410-chr15:41959320..41962249,3	MCF-7	breast:
11	chr15:41624254..41626833-chr15:41952098..41954867,2	K562	blood:
12	chr15:41853373..41858542-chr15:41950830..41955637,10	K562	blood:
13	chr15:41953002..41954735-chr15:41971952..41974245,2	MCF-7	breast:
14	chr15:41913263..41914798-chr15:41951320..41953702,2	MCF-7	breast:
15	chr15:41952704..41955677-chr15:42269856..42272362,2	K562	blood:
16	chr15:41953002..41954579-chr15:41954789..41956484,2	MCF-7	breast:
17	chr15:41952656..41953164-chr5:151150537..151151431,2	Hela-S3	cervix:
18	chr15:41952625..41954330-chr15:41973061..41975209,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000119004	Chromatin interaction
ENSG00000145907	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000092445	Chromatin interaction
ENSG00000174197	Chromatin interaction
ENSG00000259838	Chromatin interaction
ENSG00000104147	Chromatin interaction
ENSG00000137806	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1107858	0.88[ASN][1000 genomes]
rs11634956	0.88[EUR][1000 genomes]
rs11637341	0.81[ASN][1000 genomes]
rs16952372	0.84[EUR][1000 genomes]
rs16971976	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17677199	0.81[ASN][1000 genomes]
rs2004162	0.81[ASN][1000 genomes]
rs28556632	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28810086	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28850384	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924570	0.81[ASN][1000 genomes]
rs62002066	0.81[ASN][1000 genomes]
rs62003900	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171123	0.88[EUR][1000 genomes]
rs8035855	0.82[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28700954	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41951800-41953200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:41951800-41953200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:41951800-41953200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:41951800-41953200	Active TSS	Fetal Lung	lung
5	chr15:41951800-41953400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr15:41951800-41954800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr15:41951800-41955400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:41952000-41953200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:41952000-41953200	Active TSS	Brain Germinal Matrix	brain
10	chr15:41952000-41953200	Active TSS	Brain Hippocampus Middle	brain
11	chr15:41952000-41953200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr15:41952000-41953200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
13	chr15:41952000-41953400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:41952000-41953400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr15:41952000-41953400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:41952000-41953600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:41952000-41954000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr15:41952000-41954000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:41952000-41954000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:41952000-41954000	Flanking Active TSS	Right Ventricle	heart
21	chr15:41952000-41954400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:41952000-41954400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr15:41952000-41954400	Active TSS	Brain Angular Gyrus	brain
24	chr15:41952000-41954400	Active TSS	Brain Substantia Nigra	brain
25	chr15:41952000-41954400	Flanking Active TSS	Placenta	Placenta
26	chr15:41952000-41954400	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr15:41952000-41954400	Active TSS	HSMM	muscle
28	chr15:41952000-41954400	Active TSS	HSMMtube	muscle
29	chr15:41952000-41954600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr15:41952000-41954600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:41952000-41954600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:41952000-41954600	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr15:41952000-41954600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr15:41952000-41954600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr15:41952000-41954600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr15:41952000-41954600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:41952000-41954600	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr15:41952000-41954600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr15:41952000-41954600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr15:41952000-41954600	Flanking Active TSS	GM12878-XiMat	blood
41	chr15:41952000-41954600	Flanking Active TSS	Osteobl	bone
42	chr15:41952000-41954800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:41952000-41954800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:41952000-41954800	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr15:41952000-41954800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr15:41952000-41954800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr15:41952000-41954800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr15:41952000-41954800	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr15:41952000-41954800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr15:41952000-41954800	Flanking Active TSS	NH-A	brain

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