Variant report

Variant	rs4410463
Chromosome Location	chr3:47735397-47735398
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	chr3:47734956..47737818-chr3:47752172..47754463,2	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10865948	0.84[AMR][1000 genomes]
rs11130143	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130144	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130145	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130146	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130147	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130148	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707707	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708849	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11712152	0.89[EUR][1000 genomes]
rs11712464	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11714942	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11716582	0.83[AMR][1000 genomes]
rs11927129	0.91[EUR][1000 genomes]
rs12492915	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12495204	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12497921	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12498027	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12633604	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12635438	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636863	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13061412	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13063042	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064183	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13069142	0.80[EUR][1000 genomes]
rs13070035	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13081356	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13086149	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13091913	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094264	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13098128	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1403578	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1403579	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464614	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1486915	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17079785	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2030596	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2047559	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2049301	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101398	0.82[AMR][1000 genomes]
rs2133601	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140335	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293226	0.83[AMR][1000 genomes]
rs2882611	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34351471	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34569417	0.82[AMR][1000 genomes]
rs34777284	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34906469	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35148469	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35664069	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35698005	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3755637	0.85[AMR][1000 genomes]
rs3755638	0.82[AMR][1000 genomes]
rs3772399	0.86[AMR][1000 genomes]
rs3772403	0.82[AMR][1000 genomes]
rs3888	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3915654	0.86[AMR][1000 genomes]
rs4274776	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4858801	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4858803	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4858842	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858846	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858851	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858853	0.86[EUR][1000 genomes]
rs4858857	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858860	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4858863	0.80[EUR][1000 genomes]
rs55823596	0.87[EUR][1000 genomes]
rs56376646	0.93[EUR][1000 genomes]
rs60110914	0.83[AMR][1000 genomes]
rs61181421	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61620099	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61675361	0.81[EUR][1000 genomes]
rs62262129	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62263561	0.87[EUR][1000 genomes]
rs62263575	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6442072	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442074	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442079	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442081	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442082	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442083	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442085	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442086	0.83[EUR][1000 genomes]
rs6768699	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772301	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773467	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773732	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774170	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6776963	0.85[EUR][1000 genomes]
rs6777632	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6782998	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6785669	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6786001	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6789835	0.82[AMR][1000 genomes]
rs6792350	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6792497	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792737	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806860	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72906488	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73085151	0.87[EUR][1000 genomes]
rs7429162	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612219	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7613934	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7618758	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621236	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7624474	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7629850	0.80[EUR][1000 genomes]
rs7631950	0.83[AMR][1000 genomes]
rs7637372	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637950	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638103	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7642691	0.82[AMR][1000 genomes]
rs7645846	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7646982	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7649393	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868255	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs870622	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs883661	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs883662	0.81[EUR][1000 genomes]
rs883663	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9757517	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv590232	chr3:47681881-47765547	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
4	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4410463	NME6	cis	Esophagus Muscularis	GTEx
rs4410463	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs4410463	MRPS18AP1	cis	Nerve Tibial	GTEx
rs4410463	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs4410463	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs4410463	ZNF589	cis	Nerve Tibial	GTEx
rs4410463	MRPS18AP1	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47655800-47765600	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:47656600-47790800	Strong transcription	Fetal Thymus	thymus
3	chr3:47688200-47763400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:47694400-47745800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:47695200-47737200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:47700200-47757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:47701200-47765000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:47701200-47765600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:47701400-47739800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:47701600-47762200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:47701600-47800400	Strong transcription	Dnd41	blood
12	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:47702200-47790400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:47704000-47788600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:47705600-47742800	Weak transcription	Esophagus	oesophagus
16	chr3:47705800-47739200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:47707200-47737000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr3:47707200-47739400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:47707200-47780800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:47707200-47781400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:47707600-47737400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:47707600-47762600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:47708400-47737400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:47708800-47737000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:47710600-47737200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:47710600-47756600	Strong transcription	Placenta	Placenta
27	chr3:47711000-47759400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:47711200-47739400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:47711400-47757200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:47711600-47740200	Strong transcription	NH-A	brain
31	chr3:47713200-47737200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:47713200-47737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:47713600-47739600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:47714200-47736800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:47714200-47737000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:47714600-47742200	Weak transcription	Psoas Muscle	Psoas
37	chr3:47714800-47737000	Strong transcription	Primary T cells from cord blood	blood
38	chr3:47715400-47737200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:47716000-47745800	Weak transcription	Fetal Heart	heart
40	chr3:47716000-47747400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:47717800-47736200	Strong transcription	Brain Germinal Matrix	brain
42	chr3:47719000-47752000	Weak transcription	Colonic Mucosa	Colon
43	chr3:47720600-47742200	Weak transcription	Small Intestine	intestine
44	chr3:47721600-47742800	Weak transcription	Right Ventricle	heart
45	chr3:47722000-47743000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:47722000-47747200	Weak transcription	Fetal Brain Male	brain
47	chr3:47722800-47737200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:47722800-47737200	Strong transcription	Liver	Liver
49	chr3:47723000-47738400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:47723400-47766200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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