Variant report

Variant	rs14123
Chromosome Location	chr1:212534448-212534449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212526274..212530393-chr1:212532499..212537435,6	K562	blood:
2	chr1:212528811..212530393-chr1:212534364..212536971,2	K562	blood:
3	chr1:212532088..212535630-chr1:212537355..212540816,4	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1056985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863955	0.93[CEU][hapmap]
rs10863965	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap]
rs11119886	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs11119891	1.00[CEU][hapmap]
rs11119903	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11119907	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119908	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119910	0.91[CEU][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119918	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11119927	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119932	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs11119934	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap]
rs12031941	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12033979	0.80[ASN][1000 genomes]
rs12118709	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118732	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12119779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12124582	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128123	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12128965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12129267	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133582	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap]
rs12133636	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs12134074	0.84[ASN][1000 genomes]
rs12134599	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12136095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12137798	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138533	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140158	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12141427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12143853	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12145170	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12145377	0.92[CEU][hapmap]
rs12145484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12239580	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12403586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12561785	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12562618	0.84[ASN][1000 genomes]
rs1342152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1493601	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17018777	0.93[CEU][hapmap]
rs17018847	1.00[CEU][hapmap]
rs17018853	1.00[CEU][hapmap]
rs1808986	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2166155	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2236598	0.82[ASN][1000 genomes]
rs2298115	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3754142	0.83[CHB][hapmap]
rs3754144	0.95[CHB][hapmap]
rs3767867	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[ASN][1000 genomes]
rs3767868	0.95[CHB][hapmap];1.00[GIH][hapmap]
rs3820513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4548507	0.90[ASN][1000 genomes]
rs4951597	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap]
rs903119	1.00[CEU][hapmap];0.85[TSI][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs14123	PPP2R5A	cis	Whole Blood	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	chr1:212504400-212537600	Weak transcription	Psoas Muscle	Psoas
10	chr1:212508200-212545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:212508600-212541000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:212511400-212540800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:212513200-212541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:212513800-212540800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:212514400-212540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:212514600-212537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:212514800-212541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:212515200-212536400	Strong transcription	Liver	Liver
19	chr1:212523600-212550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:212524000-212541800	Strong transcription	Fetal Thymus	thymus
21	chr1:212524400-212554600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:212525000-212541600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:212525400-212536600	Strong transcription	Primary B cells from cord blood	blood
24	chr1:212525600-212541800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:212525600-212545600	Strong transcription	Primary T cells from cord blood	blood
26	chr1:212526600-212535000	Weak transcription	Fetal Brain Female	brain
27	chr1:212526600-212540600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:212526600-212540800	Weak transcription	Right Ventricle	heart
29	chr1:212526800-212538200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:212526800-212538400	Weak transcription	Aorta	Aorta
31	chr1:212526800-212540600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:212526800-212541200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:212526800-212549200	Weak transcription	Brain Germinal Matrix	brain
34	chr1:212526800-212550800	Weak transcription	HSMMtube	muscle
35	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
36	chr1:212527800-212538400	Weak transcription	Lung	lung
37	chr1:212528000-212535400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:212528000-212540600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:212528200-212536200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:212528400-212537400	Weak transcription	Spleen	Spleen
41	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
42	chr1:212529000-212550800	Weak transcription	NHLF	lung
43	chr1:212529200-212535800	Strong transcription	HepG2	liver
44	chr1:212529200-212536200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:212529400-212536200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:212529400-212536400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:212529400-212536400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:212529400-212536400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:212529400-212536600	Strong transcription	Adipose Nuclei	Adipose
50	chr1:212529400-212539200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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