Variant report

Variant	rs12916525
Chromosome Location	chr15:41900710-41900711
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	chr15:41851029..41853126-chr15:41899971..41902269,2	K562	blood:
2	chr15:41900433..41903180-chr15:41911539..41913856,2	K562	blood:

Variant related genes	Relation type
ENSG00000092445	Chromatin interaction
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	0.91[AMR][1000 genomes]
rs10152364	0.93[AMR][1000 genomes]
rs10775122	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10775123	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10775124	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11070345	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11070347	0.93[AMR][1000 genomes]
rs11632100	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11634840	0.82[AMR][1000 genomes]
rs11639146	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639249	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12148330	0.93[AMR][1000 genomes]
rs12900295	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12902548	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915325	0.93[AMR][1000 genomes]
rs12916992	0.91[AMR][1000 genomes]
rs1867416	0.88[AMR][1000 genomes]
rs1867417	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1899819	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1899820	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1899821	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2141141	0.91[AMR][1000 genomes]
rs2178004	0.93[AMR][1000 genomes]
rs2250964	0.88[AMR][1000 genomes]
rs2577953	0.88[AMR][1000 genomes]
rs2577954	0.86[AMR][1000 genomes]
rs2695169	0.84[AMR][1000 genomes]
rs4244585	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4270151	0.85[AMR][1000 genomes]
rs4465584	0.93[AMR][1000 genomes]
rs4923908	0.91[AMR][1000 genomes]
rs4924568	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4924571	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4924572	0.91[AMR][1000 genomes]
rs62002067	0.85[AMR][1000 genomes]
rs62002069	0.91[AMR][1000 genomes]
rs6493008	0.93[AMR][1000 genomes]
rs6493010	0.84[AMR][1000 genomes]
rs7169496	0.91[AMR][1000 genomes]
rs7169668	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7176474	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7177232	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7177911	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7178205	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8027390	0.93[AMR][1000 genomes]
rs8028886	0.82[AMR][1000 genomes]
rs8030179	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8034261	0.89[AMR][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
rs12916525	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41897000-41902200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:41897000-41902400	Weak transcription	HSMMtube	muscle
3	chr15:41897200-41902000	Weak transcription	K562	blood
4	chr15:41899600-41902000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:41899800-41901000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:41899800-41902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:41900000-41902000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:41900000-41902000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:41900000-41902200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:41900600-41902200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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