Variant report

Variant	rs2577947
Chromosome Location	chr15:42037570-42037571
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	chr15:42019750..42022278-chr15:42036338..42038977,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10152332	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152364	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775124	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11070345	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632100	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634840	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855017	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197670	0.81[ASN][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs1197768	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197769	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900295	0.80[EUR][1000 genomes]
rs12902548	0.80[EUR][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1648833	1.00[CEU][hapmap]
rs1648834	1.00[CEU][hapmap]
rs1648835	1.00[CEU][hapmap]
rs1672465	1.00[CEU][hapmap]
rs1672466	1.00[CEU][hapmap]
rs16972089	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs16972136	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1867416	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880937	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009310	0.85[ASN][1000 genomes]
rs2141141	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250964	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577952	0.81[ASN][1000 genomes]
rs2577953	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2605569	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605570	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695162	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695169	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695170	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918051	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950446	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4270151	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924571	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62002069	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493008	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493010	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164209	0.93[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169668	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176474	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8027390	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028886	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030179	0.83[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038148	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2577947	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr15:42027000-42037800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:42028800-42041200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:42029000-42041400	Weak transcription	Aorta	Aorta
14	chr15:42029000-42052200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:42029000-42054200	Weak transcription	Small Intestine	intestine
16	chr15:42029200-42041400	Weak transcription	NHDF-Ad	bronchial
17	chr15:42029200-42041600	Weak transcription	HMEC	breast
18	chr15:42029200-42048400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:42029400-42040800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:42030000-42038200	Weak transcription	HUVEC	blood vessel
21	chr15:42030400-42046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:42032600-42041400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:42033800-42038800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:42035000-42039600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:42035200-42039600	Weak transcription	GM12878-XiMat	blood
26	chr15:42035400-42039600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:42035400-42040200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:42035400-42040400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:42035400-42054400	Weak transcription	Pancreas	Pancrea
30	chr15:42035600-42040200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:42035600-42040200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:42035600-42040800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:42035600-42041200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:42035600-42046600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:42035800-42039600	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:42035800-42039800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:42035800-42039800	Weak transcription	Primary T cells from cord blood	blood
38	chr15:42035800-42040200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:42035800-42040200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:42035800-42040200	Weak transcription	Right Ventricle	heart
41	chr15:42035800-42040200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:42035800-42040200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:42035800-42040600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:42035800-42040600	Weak transcription	Fetal Lung	lung
45	chr15:42035800-42040600	Weak transcription	K562	blood
46	chr15:42035800-42040800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:42035800-42040800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:42035800-42040800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:42035800-42040800	Weak transcription	A549	lung
50	chr15:42035800-42040800	Weak transcription	HSMM	muscle

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