Variant report

Variant	rs12031941
Chromosome Location	chr1:212575539-212575540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1056985	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863965	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119918	0.81[ASN][1000 genomes]
rs11119927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11119932	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119934	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12033979	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12118709	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12119779	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12128123	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12133582	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12133636	0.83[ASN][1000 genomes]
rs12134599	0.85[ASN][1000 genomes]
rs12136095	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12138533	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12140158	0.83[EUR][1000 genomes]
rs12141427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12145170	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12145484	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12239580	0.97[ASN][1000 genomes]
rs12403586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12561785	0.83[EUR][1000 genomes]
rs1388033	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1388034	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs14123	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17666015	0.86[EUR][1000 genomes]
rs1808986	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1826214	0.83[EUR][1000 genomes]
rs2166155	0.98[ASN][1000 genomes]
rs3754144	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3767867	0.92[ASN][1000 genomes]
rs3767868	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3767872	0.83[AFR][1000 genomes]
rs3820513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4338424	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4548507	0.92[ASN][1000 genomes]
rs4951596	0.90[ASN][1000 genomes]
rs4951597	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59001230	0.83[AFR][1000 genomes]
rs61828751	0.83[EUR][1000 genomes]
rs74138154	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12031941	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
2	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
3	chr1:212553200-212578400	Weak transcription	K562	blood
4	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
5	chr1:212558600-212578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:212558600-212580000	Weak transcription	Left Ventricle	heart
7	chr1:212560200-212578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:212560400-212580200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:212560600-212578200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:212560600-212578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:212560600-212580200	Weak transcription	HSMMtube	muscle
12	chr1:212560600-212582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:212560600-212582000	Weak transcription	Gastric	stomach
14	chr1:212561000-212578000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:212561000-212579800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:212561000-212579800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:212561000-212580000	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:212561000-212582400	Weak transcription	Aorta	Aorta
19	chr1:212562000-212578400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:212564200-212578800	Weak transcription	Esophagus	oesophagus
21	chr1:212564600-212576200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:212564600-212577800	Weak transcription	Spleen	Spleen
23	chr1:212564600-212578600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:212564600-212579800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:212569600-212582600	Weak transcription	Ovary	ovary
26	chr1:212570400-212578800	Weak transcription	Fetal Stomach	stomach
27	chr1:212570600-212577200	Strong transcription	Fetal Thymus	thymus
28	chr1:212570600-212577800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:212570600-212578400	Weak transcription	HepG2	liver
30	chr1:212570600-212582000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:212570800-212576000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:212570800-212580000	Weak transcription	Fetal Lung	lung
33	chr1:212571000-212578600	Weak transcription	Brain Anterior Caudate	brain
34	chr1:212571000-212586200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:212571200-212576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:212571200-212578400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:212571200-212580000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:212571400-212576200	Weak transcription	Brain Substantia Nigra	brain
39	chr1:212571400-212577800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:212571400-212580000	Weak transcription	NH-A	brain
41	chr1:212571600-212577600	Strong transcription	Primary T cells from cord blood	blood
42	chr1:212571600-212578800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:212571800-212578600	Weak transcription	Fetal Brain Female	brain
44	chr1:212571800-212579800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:212572000-212576400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:212572000-212576600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:212572000-212576600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:212572000-212577800	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:212572000-212578400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:212572000-212579800	Weak transcription	Brain Germinal Matrix	brain

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