Variant report

Variant	rs12529959
Chromosome Location	chr6:167469292-167469293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10484530	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10484531	0.81[AMR][1000 genomes]
rs10946205	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10946207	0.87[EUR][1000 genomes]
rs10946208	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12178491	0.83[EUR][1000 genomes]
rs12193698	0.80[EUR][1000 genomes]
rs12203510	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208359	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12209395	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12213683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526548	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12527827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528323	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528689	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529876	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195812	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13199692	0.81[AMR][1000 genomes]
rs13204839	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13208636	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210649	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213249	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1322077	0.83[AMR][1000 genomes]
rs1358882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17524252	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17615336	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1810644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1810645	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1894603	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2001114	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2038580	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2181058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181059	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2237273	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2237276	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2237277	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2239823	0.80[EUR][1000 genomes]
rs2239826	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2239827	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282860	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2282861	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2285147	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2285148	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2301436	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239933	0.83[AMR][1000 genomes]
rs35171809	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4710175	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4710176	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62436765	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456143	0.85[AMR][1000 genomes]
rs6456146	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6456149	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456151	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456152	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6456153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456154	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6900701	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6902119	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904946	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6909180	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909475	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909502	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918286	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920858	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6921588	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6923582	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6925969	0.84[EUR][1000 genomes]
rs6929466	0.84[AMR][1000 genomes]
rs6932740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934043	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936261	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6941355	0.87[EUR][1000 genomes]
rs720325	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742305	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748224	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7749278	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7760495	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7761977	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7762156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766242	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs911632	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916331	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9295384	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295385	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9457249	0.82[AMR][1000 genomes]
rs9457251	0.82[AMR][1000 genomes]
rs9457257	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9457258	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9457260	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9457261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9457268	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9457270	0.84[EUR][1000 genomes]
rs9459835	0.82[AMR][1000 genomes]
rs9459839	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9459840	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9459841	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9459842	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9459845	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9459846	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9459853	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9459854	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9459855	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9459862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9459871	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9459872	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9459874	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
7	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
9	nsv464140	chr6:167426681-167492552	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv886943	chr6:167440244-167502638	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv2752099	chr6:167448181-167579102	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv519550	chr6:167450609-167473685	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv1841903	chr6:167459596-167489090	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	esv1824563	chr6:167461501-167489090	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	esv1837292	chr6:167461501-167489090	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	esv1840181	chr6:167461562-167489090	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12529959	AL133458.1	cis	Whole Blood	GTEx
rs12529959	RNASET2	cis	Esophagus Mucosa	GTEx
rs12529959	RNASET2	cis	Whole Blood	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167441400-167473400	Weak transcription	Psoas Muscle	Psoas
2	chr6:167449000-167470400	Weak transcription	Brain Anterior Caudate	brain
3	chr6:167455000-167470600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:167456200-167470800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:167456600-167473200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:167458400-167471200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:167460400-167469800	Weak transcription	Gastric	stomach
8	chr6:167461800-167470000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:167462000-167469800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:167464200-167469400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:167465000-167469600	Weak transcription	GM12878-XiMat	blood
12	chr6:167466000-167470800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:167466000-167472000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:167466000-167472000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:167466200-167471000	Enhancers	Primary T cells from cord blood	blood
16	chr6:167466400-167471000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr6:167466400-167471000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:167466400-167471000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:167466600-167470600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:167467000-167470600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:167467000-167470800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:167467000-167471000	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:167468400-167470800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:167468800-167471200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:167469000-167470600	Enhancers	Primary B cells from cord blood	blood
26	chr6:167469000-167472000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:167469200-167469600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:167469200-167469800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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