Variant report

Variant	rs2058560
Chromosome Location	chr12:9873689-9873690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1008610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1044771	0.91[JPT][hapmap]
rs10466829	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10492165	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10492166	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10743819	0.95[ASN][1000 genomes]
rs10743823	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10772046	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10772062	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10772070	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772071	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772072	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772073	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772074	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772079	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10772087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772090	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10772091	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772092	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772094	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772102	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10772108	0.87[ASN][1000 genomes]
rs10844380	0.83[ASN][1000 genomes]
rs10844427	0.83[EUR][1000 genomes]
rs10844456	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10844468	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10844503	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10844537	0.82[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844562	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844569	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844597	0.92[ASN][1000 genomes]
rs10844609	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844610	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844615	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844617	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10844620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844622	0.95[ASN][1000 genomes]
rs10844626	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844627	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844630	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844632	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844633	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844635	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844637	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10844638	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844639	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10844640	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844657	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844682	0.87[ASN][1000 genomes]
rs10844706	0.86[JPT][hapmap]
rs11052372	0.84[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11052423	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11052426	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11052552	0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11052582	0.81[ASN][1000 genomes]
rs11052604	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11052713	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11052717	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052750	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11052751	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11052752	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11052756	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11052877	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12227655	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12228641	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12304510	0.95[ASN][1000 genomes]
rs12317499	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427310	0.81[ASN][1000 genomes]
rs17806710	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985788	0.83[ASN][1000 genomes]
rs2012643	0.80[ASN][1000 genomes]
rs2080206	0.83[ASN][1000 genomes]
rs2080211	0.89[JPT][hapmap]
rs2098298	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2114870	0.88[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs2192437	0.96[ASN][1000 genomes]
rs2268146	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2401390	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2401393	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2401394	0.96[ASN][1000 genomes]
rs2401395	0.96[ASN][1000 genomes]
rs2895988	0.85[JPT][hapmap]
rs3764021	0.89[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs3764022	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763839	0.83[ASN][1000 genomes]
rs4763840	0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs61915473	0.81[ASN][1000 genomes]
rs7296241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7306557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7307111	0.95[ASN][1000 genomes]
rs7310460	0.91[JPT][hapmap]
rs741199	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741200	0.85[ASN][1000 genomes]
rs7956831	0.95[ASN][1000 genomes]
rs7964018	0.84[ASN][1000 genomes]
rs7968401	0.89[ASN][1000 genomes]
rs7970116	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7973535	0.96[ASN][1000 genomes]
rs7973638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7974396	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7976584	0.96[ASN][1000 genomes]
rs7977720	0.95[ASN][1000 genomes]
rs917911	0.91[JPT][hapmap]
rs917913	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv442255	chr12:9862078-9874924	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3693109	chr12:9863968-9876091	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv976571	chr12:9868953-9873977	Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2058560	PTMS	cis	parietal	SCAN
rs2058560	CLEC2A	cis	parietal	SCAN
rs2058560	LOC653113	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9861000-9874200	Weak transcription	Fetal Thymus	thymus
2	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:9861800-9874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:9868600-9879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:9869200-9874200	Weak transcription	K562	blood
7	chr12:9871000-9874000	Enhancers	Primary B cells from cord blood	blood
8	chr12:9872600-9874000	Enhancers	Hela-S3	cervix
9	chr12:9872600-9875400	Enhancers	Fetal Lung	lung
10	chr12:9872600-9875600	Enhancers	HUVEC	blood vessel
11	chr12:9872800-9874000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:9873200-9875400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:9873400-9874400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:9873400-9874400	Enhancers	Colon Smooth Muscle	Colon
15	chr12:9873400-9875000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:9873400-9875400	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:9873600-9874400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:9873600-9874400	Enhancers	NHEK	skin
19	chr12:9873600-9874600	Enhancers	Placenta	Placenta
20	chr12:9873600-9874800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr12:9873600-9875200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:9873600-9875400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:9873600-9875400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:9873600-9875400	Flanking Active TSS	A549	lung
25	chr12:9873600-9876800	Enhancers	Primary B cells from peripheral blood	blood
26	chr12:9873600-9877600	Flanking Active TSS	GM12878-XiMat	blood

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