Variant report

Variant	rs1197769
Chromosome Location	chr15:42055856-42055857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10152332	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10152364	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10775123	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10775124	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1081022	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11070345	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070347	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632100	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634840	0.89[ASN][1000 genomes]
rs11855017	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197670	0.84[ASN][1000 genomes]
rs1197704	0.83[ASN][1000 genomes]
rs1197768	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197772	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148330	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12441249	0.90[ASN][1000 genomes]
rs12915325	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916992	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16972089	0.86[EUR][1000 genomes]
rs16972136	0.84[EUR][1000 genomes]
rs1867416	0.87[ASN][1000 genomes]
rs1867417	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1880937	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880938	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1899820	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899821	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1918314	0.93[ASN][1000 genomes]
rs2009310	0.82[ASN][1000 genomes]
rs2141141	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2178004	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250964	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577947	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577950	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577951	0.97[ASN][1000 genomes]
rs2577952	0.84[ASN][1000 genomes]
rs2577953	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577954	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577955	0.90[ASN][1000 genomes]
rs2577958	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577959	0.93[ASN][1000 genomes]
rs2605569	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2605570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695162	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695163	0.97[ASN][1000 genomes]
rs2695164	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695166	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695168	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695169	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695170	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2918051	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2925337	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950446	0.86[ASN][1000 genomes]
rs3743028	0.82[ASN][1000 genomes]
rs4244585	0.81[EUR][1000 genomes]
rs4270151	0.83[ASN][1000 genomes]
rs4371125	0.90[ASN][1000 genomes]
rs4465584	0.86[ASN][1000 genomes]
rs4923908	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924568	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924571	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924572	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62002069	0.90[ASN][1000 genomes]
rs6493008	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493010	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7164209	0.90[ASN][1000 genomes]
rs7169496	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169668	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7177911	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7178205	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8027390	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8028886	0.87[ASN][1000 genomes]
rs8034261	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8038148	0.87[ASN][1000 genomes]
rs8038783	0.90[ASN][1000 genomes]
rs8039440	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1041861	chr15:42016097-42062287	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	19 gene(s)	inside rSNPs	diseases
10	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1197769	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
3	chr15:42009800-42056800	Weak transcription	Fetal Heart	heart
4	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:42035800-42058200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42036000-42058400	Weak transcription	Psoas Muscle	Psoas
9	chr15:42039000-42064400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:42039600-42062600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:42040000-42061400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:42040200-42059800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:42040200-42064400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:42040600-42063000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:42041800-42056800	Weak transcription	Esophagus	oesophagus
16	chr15:42041800-42058200	Weak transcription	Gastric	stomach
17	chr15:42042000-42057000	Weak transcription	Right Ventricle	heart
18	chr15:42042000-42057200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:42042600-42056600	Weak transcription	Aorta	Aorta
20	chr15:42042600-42056600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:42042800-42056200	Weak transcription	Brain Substantia Nigra	brain
22	chr15:42042800-42057200	Weak transcription	HUVEC	blood vessel
23	chr15:42043200-42057200	Weak transcription	NHLF	lung
24	chr15:42044400-42062600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr15:42045600-42060000	Strong transcription	Primary B cells from cord blood	blood
26	chr15:42045600-42061600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:42045600-42062000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:42045600-42065200	Weak transcription	Stomach Mucosa	stomach
29	chr15:42045800-42063200	Strong transcription	Placenta	Placenta
30	chr15:42046000-42061400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:42046000-42062600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:42046200-42062800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:42046400-42060400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr15:42047600-42057000	Weak transcription	NHDF-Ad	bronchial
35	chr15:42047600-42058600	Weak transcription	Fetal Brain Male	brain
36	chr15:42048800-42057000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:42050200-42059600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:42051000-42062400	Strong transcription	Primary T cells from cord blood	blood
39	chr15:42051000-42062400	Strong transcription	Liver	Liver
40	chr15:42051200-42061200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:42051600-42060000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:42051600-42061800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:42051600-42062400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:42051800-42059200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:42051800-42060200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:42051800-42060400	Strong transcription	Brain Germinal Matrix	brain
47	chr15:42051800-42061200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:42051800-42061800	Strong transcription	Fetal Intestine Large	intestine
49	chr15:42051800-42062400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:42051800-42062400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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