Variant report

Variant	rs12138533
Chromosome Location	chr1:212538923-212538924
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	chr1:212531780..212534376-chr1:212536682..212539871,4	K562	blood:
2	chr1:212532088..212535630-chr1:212537355..212540816,4	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1056985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119903	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11119907	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119908	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119910	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119918	0.97[ASN][1000 genomes]
rs11119927	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12031941	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12033979	0.80[ASN][1000 genomes]
rs12118709	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118732	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12119779	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12124582	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128123	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12128965	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12129267	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133636	1.00[ASN][1000 genomes]
rs12134074	0.84[ASN][1000 genomes]
rs12134599	0.99[ASN][1000 genomes]
rs12136095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12137798	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140158	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12141427	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12143853	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12145170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12145484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12239580	0.85[ASN][1000 genomes]
rs12403586	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12561785	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12562618	0.84[ASN][1000 genomes]
rs1342152	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs14123	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493601	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1808986	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2166155	0.85[ASN][1000 genomes]
rs2236598	0.82[ASN][1000 genomes]
rs2298115	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3767867	0.89[ASN][1000 genomes]
rs3820513	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4548507	0.90[ASN][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	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12138533	PPP2R5A	cis	Whole Blood	GTEx
rs12138533	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
2	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
3	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:212508200-212545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:212508600-212541000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:212511400-212540800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:212513200-212541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:212513800-212540800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:212514400-212540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:212514800-212541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:212523600-212550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:212524000-212541800	Strong transcription	Fetal Thymus	thymus
18	chr1:212524400-212554600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:212525000-212541600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:212525600-212541800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:212525600-212545600	Strong transcription	Primary T cells from cord blood	blood
22	chr1:212526600-212540600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:212526600-212540800	Weak transcription	Right Ventricle	heart
24	chr1:212526800-212540600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:212526800-212541200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:212526800-212549200	Weak transcription	Brain Germinal Matrix	brain
27	chr1:212526800-212550800	Weak transcription	HSMMtube	muscle
28	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
29	chr1:212528000-212540600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
31	chr1:212529000-212550800	Weak transcription	NHLF	lung
32	chr1:212529400-212539200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:212529400-212541200	Strong transcription	GM12878-XiMat	blood
34	chr1:212529400-212562400	Strong transcription	Dnd41	blood
35	chr1:212529600-212540400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:212529600-212541600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:212529800-212540400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:212529800-212541000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:212529800-212541600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:212530000-212540400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:212530200-212552600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:212531200-212542200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:212531400-212540400	Strong transcription	HUVEC	blood vessel
45	chr1:212531600-212550000	Weak transcription	Pancreas	Pancrea
46	chr1:212531800-212550400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:212532000-212548600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:212532200-212550400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:212532400-212560200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:212533400-212557000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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