Variant report

Variant	rs12492915
Chromosome Location	chr3:47678035-47678036
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	chr3:47671404..47674024-chr3:47676928..47679281,2	K562	blood:

Extended variants
information (count: 132 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1014228	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10865948	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130138	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130139	0.86[EUR][1000 genomes]
rs11130143	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130144	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130145	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130146	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130147	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11130148	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11707707	0.82[EUR][1000 genomes]
rs11708849	0.82[AMR][1000 genomes]
rs11712152	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11714942	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11716582	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11929303	0.92[EUR][1000 genomes]
rs12495204	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12497921	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12498027	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633604	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12635438	0.84[EUR][1000 genomes]
rs12636198	0.87[EUR][1000 genomes]
rs12636863	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13061412	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13063042	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064183	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13069142	0.96[EUR][1000 genomes]
rs13070035	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13079407	0.80[AMR][1000 genomes]
rs13081356	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13084555	0.86[AMR][1000 genomes]
rs13085978	0.93[EUR][1000 genomes]
rs13086149	0.92[AMR][1000 genomes]
rs13091913	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13094264	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13098128	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1403578	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1403579	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464614	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1486915	0.89[AMR][1000 genomes]
rs17079785	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2030596	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2047559	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049300	0.88[AFR][1000 genomes]
rs2049301	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2101398	0.83[AMR][1000 genomes]
rs2133601	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2140335	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280567	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2293226	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882611	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34252990	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34351471	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34569417	0.83[AMR][1000 genomes]
rs34616865	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34777284	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34906469	0.84[AMR][1000 genomes]
rs35148469	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35167544	0.81[EUR][1000 genomes]
rs35664069	0.86[EUR][1000 genomes]
rs35698005	0.91[AMR][1000 genomes]
rs3732530	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3755637	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755638	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3772399	0.87[AMR][1000 genomes]
rs3772403	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3888	0.84[AMR][1000 genomes]
rs3915654	0.87[AMR][1000 genomes]
rs4274776	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4410463	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858801	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858803	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858836	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4858842	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858846	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858851	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4858857	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4858860	0.84[AMR][1000 genomes]
rs56746603	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60110914	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60322343	0.87[EUR][1000 genomes]
rs61181421	0.89[AMR][1000 genomes]
rs61620099	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61675361	0.94[EUR][1000 genomes]
rs62262129	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62263575	0.82[AMR][1000 genomes]
rs6442072	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442074	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442079	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6442081	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6442082	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6442083	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6442085	0.91[AMR][1000 genomes]
rs6767896	0.84[AMR][1000 genomes]
rs6768699	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6772301	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6773467	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773732	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6774170	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6777632	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6784946	0.85[AMR][1000 genomes]
rs6785031	0.87[AMR][1000 genomes]
rs6785669	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6786001	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6789835	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6792350	0.87[AMR][1000 genomes]
rs6792497	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6792737	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6806860	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72906488	0.86[AMR][1000 genomes]
rs7429162	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612219	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7613934	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618758	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7621236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624474	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631950	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637372	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7637950	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7638103	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7642691	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7645846	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7646982	0.86[AMR][1000 genomes]
rs7649393	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs868255	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs869508	0.89[EUR][1000 genomes]
rs870622	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs883661	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs883662	0.94[EUR][1000 genomes]
rs883663	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9757517	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12492915	NME6	cis	Esophagus Muscularis	GTEx
rs12492915	MRPS18AP1	cis	Nerve Tibial	GTEx
rs12492915	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs12492915	ZNF589	cis	Nerve Tibial	GTEx
rs12492915	MRPS18AP1	cis	lung	GTEx
rs12492915	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs12492915	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 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	chr3:47635000-47686800	Strong transcription	Dnd41	blood
7	chr3:47638000-47681200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:47643600-47684800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:47653400-47678200	Strong transcription	Fetal Intestine Large	intestine
10	chr3:47654400-47707600	Weak transcription	Stomach Mucosa	stomach
11	chr3:47655000-47681000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:47655000-47681600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:47655600-47684600	Strong transcription	Liver	Liver
14	chr3:47655800-47686800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:47655800-47698800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:47655800-47765600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:47656000-47680600	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:47656200-47681600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:47656200-47699800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:47656400-47679800	Strong transcription	Thymus	Thymus
21	chr3:47656400-47693800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:47656400-47698200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:47656600-47790800	Strong transcription	Fetal Thymus	thymus
24	chr3:47657000-47690600	Weak transcription	Fetal Heart	heart
25	chr3:47657000-47700000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:47658000-47699800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:47658200-47680600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:47658800-47680800	Strong transcription	K562	blood
29	chr3:47660000-47680800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:47660400-47680600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:47661000-47681200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:47661400-47680600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:47661400-47711400	Weak transcription	Colonic Mucosa	Colon
34	chr3:47661600-47682600	Weak transcription	Aorta	Aorta
35	chr3:47661600-47688000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:47664400-47689400	Weak transcription	Psoas Muscle	Psoas
37	chr3:47666600-47680400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:47666600-47680600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:47667200-47680600	Strong transcription	Primary T cells from cord blood	blood
40	chr3:47667400-47680600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:47667400-47681200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr3:47667400-47681400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:47667400-47689800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:47668000-47680600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr3:47668200-47678800	Strong transcription	NH-A	brain
46	chr3:47668200-47679200	Strong transcription	HepG2	liver
47	chr3:47668200-47681200	Strong transcription	Primary hematopoietic stem cells	blood
48	chr3:47668200-47685000	Strong transcription	Placenta	Placenta
49	chr3:47668400-47680600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:47669000-47679400	Strong transcription	Duodenum Mucosa	Duodenum

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