Variant report

Variant	rs883661
Chromosome Location	chr3:47660101-47660102
allele	C/T
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: 131 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1014228	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10865948	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11130138	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130139	0.90[EUR][1000 genomes]
rs11130143	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130144	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130145	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130146	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130147	0.86[AMR][1000 genomes]
rs11130148	0.85[AMR][1000 genomes]
rs11708849	0.80[AMR][1000 genomes]
rs11712152	0.88[EUR][1000 genomes]
rs11714942	0.92[AMR][1000 genomes]
rs11716582	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11929303	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489865	0.80[EUR][1000 genomes]
rs12492915	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495204	0.87[AMR][1000 genomes]
rs12497921	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12498027	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12633604	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635438	0.81[EUR][1000 genomes]
rs12636198	0.91[EUR][1000 genomes]
rs12636863	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13061412	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13063042	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13064183	0.92[AMR][1000 genomes]
rs13069142	0.91[EUR][1000 genomes]
rs13070035	0.83[AMR][1000 genomes]
rs13081356	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13084555	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13085978	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13086149	0.90[AMR][1000 genomes]
rs13091913	0.86[AMR][1000 genomes]
rs13094264	0.85[AMR][1000 genomes]
rs13098128	0.89[AMR][1000 genomes]
rs1403578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464614	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486915	0.86[AMR][1000 genomes]
rs17079785	0.92[AMR][1000 genomes]
rs2030596	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2047559	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2049300	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2049301	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2101398	0.81[AMR][1000 genomes]
rs2133601	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2140335	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2280567	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2293226	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2882611	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34252990	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34351471	0.87[AMR][1000 genomes]
rs34569417	0.81[AMR][1000 genomes]
rs34616865	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34777284	0.85[AMR][1000 genomes]
rs34906469	0.82[AMR][1000 genomes]
rs35148469	0.92[AMR][1000 genomes]
rs35167544	0.84[EUR][1000 genomes]
rs35664069	0.83[EUR][1000 genomes]
rs35698005	0.89[AMR][1000 genomes]
rs36033865	0.80[EUR][1000 genomes]
rs3732530	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3755637	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755638	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772399	0.85[AMR][1000 genomes]
rs3772403	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3888	0.82[AMR][1000 genomes]
rs3915654	0.85[AMR][1000 genomes]
rs4274776	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4410463	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858801	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858803	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4858836	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4858842	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858846	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858851	0.85[AMR][1000 genomes]
rs4858857	0.89[AMR][1000 genomes]
rs4858860	0.82[AMR][1000 genomes]
rs56746603	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60110914	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60322343	0.91[EUR][1000 genomes]
rs61181421	0.86[AMR][1000 genomes]
rs61620099	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61675361	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62262129	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6442072	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442074	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442079	0.83[AMR][1000 genomes]
rs6442081	0.83[AMR][1000 genomes]
rs6442082	0.92[AMR][1000 genomes]
rs6442083	0.92[AMR][1000 genomes]
rs6442085	0.89[AMR][1000 genomes]
rs6767896	0.86[AMR][1000 genomes]
rs6768699	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6772301	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773467	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6773732	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6774170	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6777632	0.91[AMR][1000 genomes]
rs6780395	0.81[AMR][1000 genomes]
rs6784946	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6785031	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6785669	0.84[AMR][1000 genomes]
rs6786001	0.87[AMR][1000 genomes]
rs6789835	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6792350	0.85[AMR][1000 genomes]
rs6792497	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792737	0.92[AMR][1000 genomes]
rs6806860	0.87[AMR][1000 genomes]
rs72906488	0.84[AMR][1000 genomes]
rs7429162	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7612219	0.92[AMR][1000 genomes]
rs7613934	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618758	0.87[AMR][1000 genomes]
rs7621236	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7624474	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7631950	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637372	0.91[AMR][1000 genomes]
rs7637950	0.87[AMR][1000 genomes]
rs7638103	0.85[AMR][1000 genomes]
rs7642691	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7645846	0.92[AMR][1000 genomes]
rs7646982	0.84[AMR][1000 genomes]
rs7649393	0.85[AMR][1000 genomes]
rs868255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869508	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs870622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883662	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883663	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757517	0.86[AMR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs883661	ZNF589	cis	Nerve Tibial	GTEx
rs883661	MRPS18AP1	cis	Nerve Tibial	GTEx
rs883661	NME6	cis	Esophagus Muscularis	GTEx
rs883661	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs883661	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs883661	MRPS18AP1	cis	lung	GTEx
rs883661	DHX30	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:47632400-47660800	Weak transcription	Esophagus	oesophagus
7	chr3:47634200-47661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:47635000-47686800	Strong transcription	Dnd41	blood
9	chr3:47636800-47672800	Weak transcription	Small Intestine	intestine
10	chr3:47637200-47665000	Strong transcription	Primary T cells from cord blood	blood
11	chr3:47638000-47681200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:47638200-47665800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr3:47639200-47675800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:47643600-47684800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:47643800-47666400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:47644200-47676000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:47644400-47664600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr3:47644600-47663800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:47645200-47663200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:47645400-47663600	Strong transcription	HepG2	liver
21	chr3:47645800-47664600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr3:47646600-47666600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:47648000-47670600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:47651800-47660800	Weak transcription	Gastric	stomach
25	chr3:47651800-47661000	Weak transcription	Colonic Mucosa	Colon
26	chr3:47651800-47666800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:47652000-47660600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:47652000-47660600	Weak transcription	Lung	lung
29	chr3:47652400-47660200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:47653400-47660800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:47653400-47661600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:47653400-47678200	Strong transcription	Fetal Intestine Large	intestine
33	chr3:47653800-47664000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:47654200-47672400	Weak transcription	NHLF	lung
35	chr3:47654400-47660800	Weak transcription	Right Ventricle	heart
36	chr3:47654400-47707600	Weak transcription	Stomach Mucosa	stomach
37	chr3:47655000-47681000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:47655000-47681600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:47655400-47660800	Weak transcription	Pancreas	Pancrea
40	chr3:47655400-47666400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:47655400-47676600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:47655600-47660600	Weak transcription	Spleen	Spleen
43	chr3:47655600-47663400	Weak transcription	Psoas Muscle	Psoas
44	chr3:47655600-47663800	Strong transcription	Fetal Lung	lung
45	chr3:47655600-47677000	Strong transcription	Primary B cells from cord blood	blood
46	chr3:47655600-47684600	Strong transcription	Liver	Liver
47	chr3:47655800-47661200	Strong transcription	Brain Germinal Matrix	brain
48	chr3:47655800-47686800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:47655800-47698800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:47655800-47765600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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