Variant report

Variant	rs62002069
Chromosome Location	chr15:41995556-41995557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10152332	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152364	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775122	0.89[AMR][1000 genomes]
rs10775123	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775124	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070345	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070347	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632100	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634840	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11639146	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11639249	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11855017	0.81[ASN][1000 genomes]
rs1197768	0.90[ASN][1000 genomes]
rs1197769	0.90[ASN][1000 genomes]
rs1197772	0.90[ASN][1000 genomes]
rs12148330	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441249	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12900295	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12915325	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916525	0.91[AMR][1000 genomes]
rs12916992	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867416	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867417	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880937	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899819	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1899820	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899821	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918314	0.90[ASN][1000 genomes]
rs2009310	0.91[ASN][1000 genomes]
rs2141141	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178004	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250964	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577950	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577951	0.93[ASN][1000 genomes]
rs2577953	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.93[ASN][1000 genomes]
rs2577958	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577959	0.90[ASN][1000 genomes]
rs2605569	0.84[EUR][1000 genomes]
rs2605570	0.89[ASN][1000 genomes]
rs2695162	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	0.93[ASN][1000 genomes]
rs2695164	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695166	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695168	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695169	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695170	0.85[EUR][1000 genomes]
rs2918051	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2950446	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270151	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4371125	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4465584	0.98[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4923908	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924568	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924571	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924572	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002067	0.90[AMR][1000 genomes]
rs6493008	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493010	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164209	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7169496	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169668	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176474	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7177232	0.91[AMR][1000 genomes]
rs7177911	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178205	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027390	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028886	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8030179	0.89[ASN][1000 genomes]
rs8034261	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038148	0.84[ASN][1000 genomes]
rs8038783	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8039440	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62002069	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 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	chr15:41962000-42001400	Weak transcription	Gastric	stomach
3	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
7	chr15:41981600-41995800	Weak transcription	Fetal Stomach	stomach
8	chr15:41983000-42001200	Weak transcription	Ovary	ovary
9	chr15:41983200-42002600	Weak transcription	Small Intestine	intestine
10	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:41984400-42002800	Weak transcription	A549	lung
12	chr15:41984600-41999200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:41984600-41999400	Weak transcription	Thymus	Thymus
14	chr15:41984600-41999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:41984600-42000600	Weak transcription	Lung	lung
16	chr15:41984600-42001600	Weak transcription	Pancreas	Pancrea
17	chr15:41984800-41998800	Weak transcription	Left Ventricle	heart
18	chr15:41984800-41999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:41984800-42000800	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:41984800-42001200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:41984800-42001400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:41984800-42003000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:41985200-41996000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:41987600-42001200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:41988600-42001200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:41988600-42003000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:41988600-42003000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:41988800-42002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:41988800-42003000	Weak transcription	Fetal Kidney	kidney
30	chr15:41989000-41997400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:41989000-41999000	Weak transcription	Fetal Lung	lung
32	chr15:41989000-42003000	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
34	chr15:41989200-41998800	Weak transcription	Dnd41	blood
35	chr15:41989200-41999400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:41989200-41999400	Weak transcription	Placenta	Placenta
37	chr15:41989200-42000400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:41989200-42000800	Weak transcription	Psoas Muscle	Psoas
39	chr15:41989200-42000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:41989200-42001000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:41989200-42001000	Weak transcription	Brain Angular Gyrus	brain
42	chr15:41989200-42001000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:41989200-42001200	Weak transcription	Brain Anterior Caudate	brain
44	chr15:41989200-42001200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:41989200-42001200	Weak transcription	Right Ventricle	heart
46	chr15:41989200-42001600	Weak transcription	HSMMtube	muscle
47	chr15:41989200-42003000	Weak transcription	Brain Substantia Nigra	brain
48	chr15:41989200-42005000	Weak transcription	Fetal Heart	heart
49	chr15:41989200-42009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:41989400-41999400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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