Variant report

Variant	rs12486461
Chromosome Location	chr3:157847473-157847474
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10470472	0.86[EUR][1000 genomes]
rs1095636	0.87[EUR][1000 genomes]
rs1193511	0.86[EUR][1000 genomes]
rs1193513	0.86[EUR][1000 genomes]
rs1193536	0.86[EUR][1000 genomes]
rs1204957	0.87[EUR][1000 genomes]
rs12485440	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12696067	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059066	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13061378	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1581408	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1608100	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1608101	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1609525	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1609526	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1610266	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1610267	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1610268	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1724666	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1724679	0.87[EUR][1000 genomes]
rs1729998	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1730008	0.85[EUR][1000 genomes]
rs1730029	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1730032	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1730039	0.86[EUR][1000 genomes]
rs1730041	0.85[EUR][1000 genomes]
rs1730044	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1730099	0.88[EUR][1000 genomes]
rs1915935	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682402	0.87[EUR][1000 genomes]
rs2682407	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2693540	0.87[EUR][1000 genomes]
rs2693546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4261830	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4317053	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4346508	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4414801	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4431056	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4602343	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4622858	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4642075	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680411	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680412	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680413	0.97[ASN][1000 genomes]
rs57665991	0.97[ASN][1000 genomes]
rs6441174	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6762706	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6770442	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773505	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6783175	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6789448	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6790608	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6794461	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797626	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6803532	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803630	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs696715	0.88[EUR][1000 genomes]
rs698975	0.87[EUR][1000 genomes]
rs698976	0.88[EUR][1000 genomes]
rs698977	0.88[EUR][1000 genomes]
rs698979	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698981	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698982	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698983	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698984	0.86[EUR][1000 genomes]
rs698985	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs698992	0.87[EUR][1000 genomes]
rs699918	0.87[EUR][1000 genomes]
rs699923	0.88[EUR][1000 genomes]
rs699925	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs699926	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7614572	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618071	0.83[EUR][1000 genomes]
rs7622971	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7624303	0.97[ASN][1000 genomes]
rs7630176	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7647342	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653039	0.90[EUR][1000 genomes]
rs827104	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs827130	0.87[EUR][1000 genomes]
rs827139	0.87[EUR][1000 genomes]
rs827141	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827142	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827145	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827146	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs827147	0.86[EUR][1000 genomes]
rs827149	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827153	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827155	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827157	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827160	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827162	0.86[EUR][1000 genomes]
rs827168	0.86[EUR][1000 genomes]
rs827170	0.86[EUR][1000 genomes]
rs827173	0.87[EUR][1000 genomes]
rs827174	0.87[EUR][1000 genomes]
rs827801	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827805	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs844141	0.85[EUR][1000 genomes]
rs860422	0.89[EUR][1000 genomes]
rs862352	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs864331	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs864876	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs866657	0.88[EUR][1000 genomes]
rs9290020	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9290021	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814942	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820954	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848433	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862337	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9870745	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871021	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9881063	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9883891	0.81[AMR][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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12486461	RP11-538P18.2	cis	Artery Tibial	GTEx
rs12486461	RP11-538P18.2	cis	lung	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157828600-157847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:157828600-157857000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:157828800-157847600	Weak transcription	NH-A	brain
4	chr3:157828800-157851000	Weak transcription	Right Ventricle	heart
5	chr3:157829000-157849400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:157829200-157861400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:157830000-157866400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:157833200-157856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:157836000-157851600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:157836400-157849400	Weak transcription	NHLF	lung
11	chr3:157836600-157854600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:157837600-157877600	Weak transcription	Fetal Heart	heart
13	chr3:157838800-157862600	Weak transcription	Pancreas	Pancrea
14	chr3:157840000-157850200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:157840200-157856000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:157840800-157856200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:157841000-157848000	Strong transcription	Liver	Liver
18	chr3:157841000-157848200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:157841200-157850000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:157841400-157848200	Strong transcription	Primary B cells from cord blood	blood
21	chr3:157841400-157848600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:157841400-157849600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:157842800-157851800	Weak transcription	Brain Germinal Matrix	brain
24	chr3:157842800-157855600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:157842800-157855600	Weak transcription	Fetal Stomach	stomach
26	chr3:157842800-157855800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:157842800-157856400	Weak transcription	Placenta	Placenta
28	chr3:157842800-157856800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:157842800-157858000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:157842800-157858200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:157843000-157868600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:157843400-157856600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:157843600-157857200	Weak transcription	HepG2	liver
34	chr3:157843600-157866200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:157843600-157886800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:157843800-157849600	ZNF genes & repeats	GM12878-XiMat	blood
37	chr3:157845600-157848000	Strong transcription	Thymus	Thymus
38	chr3:157845600-157848200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:157845600-157848400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:157845800-157854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:157845800-157857600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:157846000-157848200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:157846000-157848200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:157846000-157848400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:157846000-157849400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:157846000-157849400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:157846000-157849400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:157846000-157850600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:157846000-157851600	Weak transcription	Fetal Kidney	kidney
50	chr3:157846000-157851800	Weak transcription	Fetal Brain Male	brain

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