Variant report

Variant	rs62002066
Chromosome Location	chr15:41986411-41986412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070343	0.82[ASN][1000 genomes]
rs1107858	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634956	0.81[ASN][1000 genomes]
rs11637341	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440747	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16971976	0.93[ASN][1000 genomes]
rs17677199	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677991	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17678138	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17678552	0.84[ASN][1000 genomes]
rs17734856	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2004162	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412622	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2577960	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28444909	0.89[EUR][1000 genomes]
rs28556632	0.93[ASN][1000 genomes]
rs28700954	0.81[ASN][1000 genomes]
rs28810086	0.93[ASN][1000 genomes]
rs28850384	0.93[ASN][1000 genomes]
rs4924570	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003900	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62002066	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
2	chr15:41955000-41988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:41959400-41988600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:41959400-41989000	Weak transcription	NHDF-Ad	bronchial
5	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:41962000-41988400	Weak transcription	Adipose Nuclei	Adipose
7	chr15:41962000-41990800	Weak transcription	NH-A	brain
8	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:41962000-42001400	Weak transcription	Gastric	stomach
10	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:41962600-41988400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:41963400-41988400	Weak transcription	Placenta	Placenta
13	chr15:41963600-41987800	Weak transcription	Primary B cells from cord blood	blood
14	chr15:41966600-41988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:41968800-41988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:41971600-41988200	Weak transcription	Fetal Thymus	thymus
17	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:41972000-41989600	Weak transcription	Fetal Intestine Small	intestine
19	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
21	chr15:41973200-41988400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:41975800-41988400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:41976000-41988000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:41976800-41988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:41978800-41991200	Weak transcription	Liver	Liver
26	chr15:41980600-41987400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:41980600-41988200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:41980800-41988400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:41981000-41988400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:41981200-41988400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:41981600-41988400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:41981600-41988400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:41981600-41995800	Weak transcription	Fetal Stomach	stomach
34	chr15:41982400-41988200	Weak transcription	Brain Substantia Nigra	brain
35	chr15:41983000-42001200	Weak transcription	Ovary	ovary
36	chr15:41983200-41988400	Weak transcription	Brain Anterior Caudate	brain
37	chr15:41983200-42002600	Weak transcription	Small Intestine	intestine
38	chr15:41984000-41988000	Weak transcription	GM12878-XiMat	blood
39	chr15:41984200-41987600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:41984200-41987600	Weak transcription	HUVEC	blood vessel
41	chr15:41984200-41988200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:41984200-41988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:41984200-41990600	Weak transcription	Fetal Intestine Large	intestine
44	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:41984400-41988000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:41984400-41988400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:41984400-42002800	Weak transcription	A549	lung
48	chr15:41984600-41987200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr15:41984600-41988000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:41984600-41988000	Weak transcription	Primary T cells from cord blood	blood

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