Variant report

Variant	rs2695162
Chromosome Location	chr15:42039902-42039903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42039177..42040902-chr15:42043568..42045872,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10152332	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152364	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775123	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775124	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1081022	0.82[EUR][1000 genomes]
rs11070345	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070347	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632100	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634840	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855017	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197670	0.81[ASN][1000 genomes]
rs1197768	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197769	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197772	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148330	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441249	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900295	0.81[EUR][1000 genomes]
rs12915325	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916992	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16972089	0.86[EUR][1000 genomes]
rs16972136	0.82[EUR][1000 genomes]
rs1867416	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867417	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880937	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1899819	0.80[EUR][1000 genomes]
rs1899820	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1899821	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1918314	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009310	0.85[ASN][1000 genomes]
rs2141141	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178004	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250964	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577950	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577952	0.81[ASN][1000 genomes]
rs2577953	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577959	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2605569	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605570	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695163	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695164	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695166	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695168	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695169	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695170	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918051	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950446	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4270151	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4371125	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4465584	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4923908	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924568	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924571	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924572	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62002069	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493008	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493010	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164209	0.93[ASN][1000 genomes]
rs7169496	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169668	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176474	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7177911	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178205	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8027390	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028886	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030179	0.83[ASN][1000 genomes]
rs8034261	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038148	0.90[ASN][1000 genomes]
rs8038783	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039440	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
4	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
5	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
6	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
7	nsv1044347	chr15:42023805-42049360	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2695162	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	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
3	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
4	chr15:42006400-42041400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:42009800-42056800	Weak transcription	Fetal Heart	heart
6	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:42025000-42045800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:42025800-42045000	Weak transcription	Stomach Mucosa	stomach
11	chr15:42028800-42041200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:42029000-42041400	Weak transcription	Aorta	Aorta
13	chr15:42029000-42052200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:42029000-42054200	Weak transcription	Small Intestine	intestine
15	chr15:42029200-42041400	Weak transcription	NHDF-Ad	bronchial
16	chr15:42029200-42041600	Weak transcription	HMEC	breast
17	chr15:42029200-42048400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:42029400-42040800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:42030400-42046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:42032600-42041400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:42035400-42040200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:42035400-42040400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:42035400-42054400	Weak transcription	Pancreas	Pancrea
24	chr15:42035600-42040200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:42035600-42040200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:42035600-42040800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:42035600-42041200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:42035600-42046600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:42035800-42040200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:42035800-42040200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:42035800-42040200	Weak transcription	Right Ventricle	heart
32	chr15:42035800-42040200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:42035800-42040200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:42035800-42040600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:42035800-42040600	Weak transcription	Fetal Lung	lung
36	chr15:42035800-42040600	Weak transcription	K562	blood
37	chr15:42035800-42040800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:42035800-42040800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:42035800-42040800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:42035800-42040800	Weak transcription	A549	lung
41	chr15:42035800-42040800	Weak transcription	HSMM	muscle
42	chr15:42035800-42040800	Weak transcription	NHLF	lung
43	chr15:42035800-42041000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:42035800-42041000	Weak transcription	Brain Angular Gyrus	brain
45	chr15:42035800-42041000	Weak transcription	HSMMtube	muscle
46	chr15:42035800-42041000	Weak transcription	NH-A	brain
47	chr15:42035800-42041200	Weak transcription	Fetal Kidney	kidney
48	chr15:42035800-42041400	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:42035800-42047600	Weak transcription	NHEK	skin
50	chr15:42035800-42058200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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