Variant report

Variant	rs2030596
Chromosome Location	chr3:47743202-47743203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10865948	0.87[AMR][1000 genomes]
rs11130138	0.83[AMR][1000 genomes]
rs11130143	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130144	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130145	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130146	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130147	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130148	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130150	0.80[AFR][1000 genomes]
rs11707707	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11708849	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712152	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11712464	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714942	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716582	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11927129	0.91[EUR][1000 genomes]
rs12492915	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495204	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12497921	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12498027	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12633604	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635438	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12636863	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13061412	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13063042	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13064183	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13069142	0.80[EUR][1000 genomes]
rs13070035	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13077230	0.81[AFR][1000 genomes]
rs13079407	0.80[AMR][1000 genomes]
rs13081356	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13084555	0.82[AMR][1000 genomes]
rs13086149	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091913	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13094264	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13098128	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1403578	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1403579	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1464614	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1486915	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17079785	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2047559	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049301	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2101398	0.83[AMR][1000 genomes]
rs2133601	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2140335	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293226	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2882611	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34351471	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34569417	0.83[AMR][1000 genomes]
rs34777284	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34906469	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35148469	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35582375	0.81[AFR][1000 genomes]
rs35664069	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35698005	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3755637	0.84[AMR][1000 genomes]
rs3755638	0.87[AMR][1000 genomes]
rs3772399	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3772403	0.87[AMR][1000 genomes]
rs3888	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3915654	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4274776	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4410463	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858801	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4858803	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4858836	0.83[AMR][1000 genomes]
rs4858842	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858846	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858851	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858853	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858857	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858860	0.84[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];0.82[ASN][1000 genomes]
rs56746603	0.85[AMR][1000 genomes]
rs60110914	0.82[AMR][1000 genomes]
rs61181421	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61620099	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61675361	0.81[EUR][1000 genomes]
rs62262129	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62263561	0.87[EUR][1000 genomes]
rs62263575	0.82[AMR][1000 genomes]
rs6442072	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442074	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442079	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442081	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442082	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442083	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442085	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442086	0.83[EUR][1000 genomes]
rs6768699	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6772301	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773467	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773732	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6774170	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6776963	0.85[EUR][1000 genomes]
rs6777632	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6782998	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6784946	0.81[AMR][1000 genomes]
rs6785031	0.83[AMR][1000 genomes]
rs6785669	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786001	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6789835	0.81[AMR][1000 genomes]
rs6792350	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6792497	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792737	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6806860	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72906488	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73085151	0.87[EUR][1000 genomes]
rs7429162	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612219	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7613934	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618758	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621236	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7624474	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7629850	0.80[EUR][1000 genomes]
rs7631950	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7637372	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7637950	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7638103	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642691	0.81[AMR][1000 genomes]
rs7645846	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7646982	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7649393	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs868255	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs870622	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883661	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883662	0.81[EUR][1000 genomes]
rs883663	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9757517	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2030596	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs2030596	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs2030596	NME6	cis	Esophagus Muscularis	GTEx
rs2030596	ZNF589	cis	Nerve Tibial	GTEx
rs2030596	MRPS18AP1	cis	lung	GTEx
rs2030596	MRPS18AP1	cis	Artery Tibial	GTEx
rs2030596	MRPS18AP1	cis	Nerve Tibial	GTEx
rs2030596	MRPS18AP1	cis	Muscle Skeletal	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	chr3:47700200-47757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:47701200-47765000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:47701200-47765600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:47701600-47762200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:47701600-47800400	Strong transcription	Dnd41	blood
10	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:47702200-47790400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:47704000-47788600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:47707200-47780800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:47707200-47781400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:47707600-47762600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:47710600-47756600	Strong transcription	Placenta	Placenta
17	chr3:47711000-47759400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:47711400-47757200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:47716000-47745800	Weak transcription	Fetal Heart	heart
20	chr3:47716000-47747400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:47719000-47752000	Weak transcription	Colonic Mucosa	Colon
22	chr3:47722000-47747200	Weak transcription	Fetal Brain Male	brain
23	chr3:47723400-47766200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:47727600-47745600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:47727600-47747400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:47728800-47762800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr3:47731000-47746200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:47731600-47745800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:47731800-47743600	Weak transcription	Ovary	ovary
31	chr3:47733200-47744200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:47735000-47745800	Weak transcription	NHLF	lung
33	chr3:47736600-47745600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:47736800-47745000	Weak transcription	A549	lung
35	chr3:47737200-47744000	Weak transcription	Gastric	stomach
36	chr3:47737200-47745600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:47738000-47755800	Strong transcription	Osteobl	bone
38	chr3:47738000-47772600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:47738200-47746400	Strong transcription	Primary B cells from cord blood	blood
40	chr3:47738200-47746800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:47738200-47762800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:47738200-47779600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:47738400-47745000	Strong transcription	HUVEC	blood vessel
44	chr3:47738400-47766800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:47738800-47747200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:47739000-47755200	Weak transcription	Aorta	Aorta
47	chr3:47739000-47761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:47739200-47747400	Weak transcription	Lung	lung
49	chr3:47739600-47762400	Strong transcription	GM12878-XiMat	blood
50	chr3:47739800-47744000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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