Variant report

Variant	rs883662
Chromosome Location	chr3:47660832-47660833
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47656844..47659037-chr3:47659950..47662348,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1014228	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs10865948	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs11130138	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11130139	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11130143	1.00[CEU][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130144	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130145	0.87[EUR][1000 genomes]
rs11130146	1.00[CEU][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs11130148	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs11707707	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11711725	1.00[YRI][hapmap]
rs11712152	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11716582	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927129	0.94[AMR][1000 genomes]
rs11929303	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489865	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12492915	0.94[EUR][1000 genomes]
rs12495204	0.96[CEU][hapmap];0.93[JPT][hapmap]
rs12497921	0.86[EUR][1000 genomes]
rs12498027	0.88[EUR][1000 genomes]
rs12633604	0.83[EUR][1000 genomes]
rs12635438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12636198	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12636863	0.91[EUR][1000 genomes]
rs13061412	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13063042	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs13069142	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13081356	0.87[EUR][1000 genomes]
rs13084555	0.82[EUR][1000 genomes]
rs13085978	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091913	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs13094264	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1403578	1.00[CEU][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1403579	1.00[CEU][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1464614	1.00[CEU][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1486915	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1486916	1.00[YRI][hapmap]
rs17079785	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs2030596	0.81[EUR][1000 genomes]
rs2047559	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2049300	0.83[EUR][1000 genomes]
rs2049301	0.83[EUR][1000 genomes]
rs2133601	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2140335	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs2280567	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2293226	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2351248	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap]
rs2882611	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs34252990	0.93[EUR][1000 genomes]
rs34616865	0.94[EUR][1000 genomes]
rs35167544	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35664069	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36033865	0.80[EUR][1000 genomes]
rs3732530	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3755637	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3755638	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3772403	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3888	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs4274776	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4410463	0.81[EUR][1000 genomes]
rs4858801	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858836	0.83[EUR][1000 genomes]
rs4858842	1.00[CEU][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858846	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs4858851	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs4858853	0.91[AMR][1000 genomes]
rs4858860	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs4858863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs55823596	0.91[AMR][1000 genomes]
rs56376646	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs56746603	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60110914	0.90[EUR][1000 genomes]
rs60322343	0.91[EUR][1000 genomes]
rs61620099	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61675361	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262084	0.81[AFR][1000 genomes]
rs62263561	0.91[AMR][1000 genomes]
rs6442072	0.94[EUR][1000 genomes]
rs6442074	0.83[EUR][1000 genomes]
rs6442082	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs6442086	0.89[AMR][1000 genomes]
rs6768699	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs6772301	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs6773467	0.83[EUR][1000 genomes]
rs6773732	0.83[EUR][1000 genomes]
rs6774170	1.00[CEU][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes]
rs6776963	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs6777632	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs6784946	0.81[EUR][1000 genomes]
rs6785031	0.82[EUR][1000 genomes]
rs6785669	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs6786001	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs6789835	0.83[EUR][1000 genomes]
rs6792497	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs6806860	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs73085151	0.91[AMR][1000 genomes]
rs7429162	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs7613934	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs7618758	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs7621236	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs7624474	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs7629850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7631950	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7638103	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs7642691	0.83[EUR][1000 genomes]
rs7645846	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs868255	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs869508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs870622	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883661	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883663	1.00[CEU][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9681917	1.00[CEU][hapmap];0.93[JPT][hapmap]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs883662	ZNF589	cis	Nerve Tibial	GTEx
rs883662	MRPS18AP1	cis	Artery Tibial	GTEx
rs883662	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs883662	NME6	cis	Esophagus Muscularis	GTEx
rs883662	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs883662	MRPS18AP1	cis	Nerve Tibial	GTEx
rs883662	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs883662	MRPS18AP1	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47626200-47698600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:47626400-47680600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:47626600-47688600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:47626600-47699800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:47626800-47680800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr3:47634200-47661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:47635000-47686800	Strong transcription	Dnd41	blood
8	chr3:47636800-47672800	Weak transcription	Small Intestine	intestine
9	chr3:47637200-47665000	Strong transcription	Primary T cells from cord blood	blood
10	chr3:47638000-47681200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:47638200-47665800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:47639200-47675800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:47643600-47684800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:47643800-47666400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:47644200-47676000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr3:47644400-47664600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:47644600-47663800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:47645200-47663200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:47645400-47663600	Strong transcription	HepG2	liver
20	chr3:47645800-47664600	Strong transcription	Primary hematopoietic stem cells	blood
21	chr3:47646600-47666600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:47648000-47670600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:47651800-47661000	Weak transcription	Colonic Mucosa	Colon
24	chr3:47651800-47666800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:47653400-47661600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:47653400-47678200	Strong transcription	Fetal Intestine Large	intestine
27	chr3:47653800-47664000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:47654200-47672400	Weak transcription	NHLF	lung
29	chr3:47654400-47707600	Weak transcription	Stomach Mucosa	stomach
30	chr3:47655000-47681000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:47655000-47681600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:47655400-47666400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:47655400-47676600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:47655600-47663400	Weak transcription	Psoas Muscle	Psoas
35	chr3:47655600-47663800	Strong transcription	Fetal Lung	lung
36	chr3:47655600-47677000	Strong transcription	Primary B cells from cord blood	blood
37	chr3:47655600-47684600	Strong transcription	Liver	Liver
38	chr3:47655800-47661200	Strong transcription	Brain Germinal Matrix	brain
39	chr3:47655800-47686800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:47655800-47698800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:47655800-47765600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:47656000-47662400	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr3:47656000-47666600	Strong transcription	GM12878-XiMat	blood
44	chr3:47656000-47669000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr3:47656000-47680600	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:47656200-47681600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:47656200-47699800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:47656400-47664000	Strong transcription	Adipose Nuclei	Adipose
49	chr3:47656400-47665000	Strong transcription	HSMM	muscle
50	chr3:47656400-47665600	Strong transcription	Fetal Muscle Trunk	muscle

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