Variant report

Variant	rs11629678
Chromosome Location	chr15:41932530-41932531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11070343	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11639043	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16952372	0.85[ASN][1000 genomes]
rs17676742	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17677199	0.81[AFR][1000 genomes]
rs17733613	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28526689	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28708888	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4923905	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924564	0.83[ASN][1000 genomes]
rs8023311	0.86[ASN][1000 genomes]
rs9672298	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672360	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672671	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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
rs11629678	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 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	chr15:41924600-41934200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41924800-41937400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:41924800-41940400	Weak transcription	Brain Substantia Nigra	brain
6	chr15:41924800-41940400	Weak transcription	Fetal Kidney	kidney
7	chr15:41925000-41935000	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:41925000-41937600	Weak transcription	Pancreas	Pancrea
9	chr15:41925000-41938000	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:41925000-41952200	Weak transcription	Ovary	ovary
11	chr15:41927000-41938800	Weak transcription	A549	lung
12	chr15:41927000-41939400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:41927000-41951800	Weak transcription	Hela-S3	cervix
14	chr15:41927200-41935600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:41927200-41939000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:41929800-41940400	Weak transcription	Fetal Intestine Small	intestine
17	chr15:41929800-41940800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:41930000-41939400	Weak transcription	HepG2	liver
19	chr15:41931200-41941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:41931800-41932800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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