Variant report

Variant	rs12900295
Chromosome Location	chr15:41927449-41927450
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	chr15:41926831..41929447-chr15:41939833..41942397,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10152332	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10152364	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10775122	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10775123	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10775124	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070345	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070347	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632100	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11634840	0.84[AMR][1000 genomes]
rs11639146	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11639249	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12148330	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12441249	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12915325	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12916525	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12916992	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867416	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1867417	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1880937	0.81[EUR][1000 genomes]
rs1880938	0.82[EUR][1000 genomes]
rs1899819	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1899820	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1899821	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2141141	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2178004	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2250964	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2577947	0.80[EUR][1000 genomes]
rs2577950	0.81[EUR][1000 genomes]
rs2577953	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2577954	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2577958	0.80[EUR][1000 genomes]
rs2695162	0.81[EUR][1000 genomes]
rs2695164	0.80[EUR][1000 genomes]
rs2695166	0.82[EUR][1000 genomes]
rs2695169	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2918051	0.82[EUR][1000 genomes]
rs4244585	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4270151	0.83[AMR][1000 genomes]
rs4371125	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4465584	0.91[AMR][1000 genomes]
rs4923908	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924568	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924571	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924572	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62002067	0.83[AMR][1000 genomes]
rs62002069	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6493008	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6493010	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7164209	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7169496	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7169668	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7176474	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177232	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177911	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7178205	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8027390	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8028886	0.84[AMR][1000 genomes]
rs8030179	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034261	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8038783	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8039440	0.81[AMR][1000 genomes];0.81[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
rs12900295	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41913800-41939400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:41914200-41935800	Weak transcription	Gastric	stomach
3	chr15:41922000-41929200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:41923800-41929200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:41924600-41934200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41924800-41937400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:41924800-41940400	Weak transcription	Brain Substantia Nigra	brain
8	chr15:41924800-41940400	Weak transcription	Fetal Kidney	kidney
9	chr15:41925000-41927600	Weak transcription	Left Ventricle	heart
10	chr15:41925000-41929200	Weak transcription	Fetal Intestine Large	intestine
11	chr15:41925000-41929200	Weak transcription	Fetal Intestine Small	intestine
12	chr15:41925000-41935000	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:41925000-41937600	Weak transcription	Pancreas	Pancrea
14	chr15:41925000-41938000	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:41925000-41952200	Weak transcription	Ovary	ovary
16	chr15:41927000-41929000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:41927000-41929000	Weak transcription	HepG2	liver
18	chr15:41927000-41938800	Weak transcription	A549	lung
19	chr15:41927000-41939400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:41927000-41951800	Weak transcription	Hela-S3	cervix
21	chr15:41927200-41927800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:41927200-41935600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:41927200-41939000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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