Variant report

Variant	rs28708888
Chromosome Location	chr15:41898885-41898886
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41897965..41900106-chr15:41951801..41954247,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11070343	0.87[EUR][1000 genomes]
rs11629678	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11639043	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17676742	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17733613	0.92[EUR][1000 genomes]
rs28526689	0.88[EUR][1000 genomes]
rs4923905	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9672298	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9672360	0.94[EUR][1000 genomes]
rs9672671	0.85[AFR][1000 genomes];0.93[EUR][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
rs28708888	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41896600-41899600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:41896800-41899200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:41896800-41899200	Weak transcription	HSMM	muscle
4	chr15:41896800-41899400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:41897000-41899000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:41897000-41899200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:41897000-41899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:41897000-41899200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:41897000-41899200	Weak transcription	HMEC	breast
10	chr15:41897000-41899200	Weak transcription	NHEK	skin
11	chr15:41897000-41902200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:41897000-41902400	Weak transcription	HSMMtube	muscle
13	chr15:41897200-41899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:41897200-41899200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:41897200-41899200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:41897200-41899200	Weak transcription	NHDF-Ad	bronchial
17	chr15:41897200-41899600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:41897200-41900000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:41897200-41902000	Weak transcription	K562	blood
20	chr15:41897400-41900000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:41897800-41899200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:41898000-41899200	Weak transcription	NH-A	brain
23	chr15:41898000-41899200	Weak transcription	Osteobl	bone
24	chr15:41898200-41899200	Weak transcription	NHLF	lung
25	chr15:41898600-41899800	Weak transcription	Placenta	Placenta
26	chr15:41898800-41900400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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