Variant report

Variant	rs12498027
Chromosome Location	chr3:47697664-47697665
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	chr3:47689489..47692026-chr3:47696833..47699675,2	K562	blood:
2	chr3:47694842..47697833-chr3:47842535..47844338,2	MCF-7	breast:

Extended variants
information (count: 138 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1014228	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10865948	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130138	0.85[AMR][1000 genomes]
rs11130139	0.80[EUR][1000 genomes]
rs11130143	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130144	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130145	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130146	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130147	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130148	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11707707	0.87[EUR][1000 genomes]
rs11708849	0.85[AMR][1000 genomes]
rs11712152	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712464	0.82[EUR][1000 genomes]
rs11714942	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11716582	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11929303	0.86[EUR][1000 genomes]
rs12492915	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12495204	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12497921	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12633604	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635438	0.89[EUR][1000 genomes]
rs12636198	0.82[EUR][1000 genomes]
rs12636863	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13061412	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063042	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13064183	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13069142	0.90[EUR][1000 genomes]
rs13070035	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13077230	0.81[AMR][1000 genomes]
rs13079407	0.82[AMR][1000 genomes]
rs13081356	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084555	0.84[AMR][1000 genomes]
rs13085978	0.87[EUR][1000 genomes]
rs13086149	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs13091913	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13094264	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13098128	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1403578	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1403579	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1464614	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1486915	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17079785	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2030596	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2047559	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2049300	0.82[AFR][1000 genomes]
rs2049301	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2101398	0.85[AMR][1000 genomes]
rs2133601	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2140335	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280567	0.81[EUR][1000 genomes]
rs2293226	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2882611	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34252990	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34351471	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34569417	0.85[AMR][1000 genomes]
rs34616865	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34777284	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34906469	0.86[AMR][1000 genomes]
rs35148469	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35582375	0.81[AMR][1000 genomes]
rs35664069	0.91[EUR][1000 genomes]
rs35698005	0.93[AMR][1000 genomes]
rs3732530	0.81[EUR][1000 genomes]
rs3755637	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755638	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3772399	0.90[AMR][1000 genomes]
rs3772403	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3888	0.86[AMR][1000 genomes]
rs3915654	0.90[AMR][1000 genomes]
rs4274776	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4410463	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858801	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858803	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858836	0.85[AMR][1000 genomes]
rs4858842	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858846	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858851	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858857	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4858860	0.86[AMR][1000 genomes]
rs56376646	0.82[EUR][1000 genomes]
rs56746603	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60110914	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60322343	0.81[EUR][1000 genomes]
rs61181421	0.91[AMR][1000 genomes]
rs61620099	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61675361	0.88[EUR][1000 genomes]
rs62262129	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62263575	0.84[AMR][1000 genomes]
rs6442072	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442074	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442079	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6442081	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442082	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6442083	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6442085	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6767896	0.82[AMR][1000 genomes]
rs6768699	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772301	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773467	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6773732	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6774170	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6777632	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6782998	0.81[AMR][1000 genomes]
rs6784946	0.83[AMR][1000 genomes]
rs6785031	0.85[AMR][1000 genomes]
rs6785669	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6786001	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6789835	0.81[AMR][1000 genomes]
rs6792350	0.90[AMR][1000 genomes]
rs6792497	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792737	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6806860	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72906488	0.89[AMR][1000 genomes]
rs7429162	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7612219	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7613934	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618758	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621236	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7624474	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631950	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637372	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7637950	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7638103	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7642691	0.81[AMR][1000 genomes]
rs7645846	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7646982	0.89[AMR][1000 genomes]
rs7649393	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs868255	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs869508	0.83[EUR][1000 genomes]
rs870622	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883661	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883662	0.88[EUR][1000 genomes]
rs883663	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9757517	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12498027	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs12498027	ZNF589	cis	Nerve Tibial	GTEx
rs12498027	NME6	cis	Esophagus Muscularis	GTEx
rs12498027	MRPS18AP1	cis	Nerve Tibial	GTEx
rs12498027	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs12498027	MRPS18AP1	cis	lung	GTEx
rs12498027	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 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	chr3:47626600-47699800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:47654400-47707600	Weak transcription	Stomach Mucosa	stomach
4	chr3:47655800-47698800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:47655800-47765600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:47656200-47699800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:47656400-47698200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47656600-47790800	Strong transcription	Fetal Thymus	thymus
9	chr3:47657000-47700000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:47658000-47699800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:47661400-47711400	Weak transcription	Colonic Mucosa	Colon
12	chr3:47672000-47718600	Weak transcription	Right Ventricle	heart
13	chr3:47673200-47700200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:47673600-47719200	Weak transcription	Small Intestine	intestine
15	chr3:47674200-47705000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:47675000-47703800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:47677200-47707400	Weak transcription	HMEC	breast
18	chr3:47677200-47715400	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:47677200-47720000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:47677400-47711600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:47677600-47700000	Weak transcription	NHDF-Ad	bronchial
22	chr3:47677800-47704600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:47677800-47712000	Weak transcription	Brain Angular Gyrus	brain
24	chr3:47678000-47698800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:47678000-47717800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:47680400-47699200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:47680600-47699600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:47682200-47704200	Strong transcription	Primary B cells from cord blood	blood
29	chr3:47682600-47699000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:47682600-47700200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:47683000-47703800	Weak transcription	Esophagus	oesophagus
32	chr3:47684200-47711800	Weak transcription	Ovary	ovary
33	chr3:47684400-47702200	Weak transcription	NHLF	lung
34	chr3:47684600-47699000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:47684600-47699400	Weak transcription	HUVEC	blood vessel
36	chr3:47684600-47699800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:47684600-47705200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:47684800-47697800	Weak transcription	Fetal Kidney	kidney
39	chr3:47684800-47699000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:47684800-47703800	Weak transcription	Lung	lung
41	chr3:47684800-47705200	Weak transcription	Aorta	Aorta
42	chr3:47684800-47718400	Weak transcription	Spleen	Spleen
43	chr3:47685000-47699000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:47685000-47699400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:47685800-47699800	Strong transcription	Primary T cells from cord blood	blood
46	chr3:47686000-47699800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:47687400-47699000	Weak transcription	Osteobl	bone
48	chr3:47687400-47699800	Weak transcription	NHEK	skin
49	chr3:47688200-47701200	Strong transcription	Dnd41	blood
50	chr3:47688200-47704200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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