Variant report

Variant	rs12145170
Chromosome Location	chr1:212555441-212555442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212548396..212552681-chr1:212553193..212556963,6	K562	blood:
2	chr1:212554284..212555829-chr1:212557372..212559649,2	K562	blood:
3	chr1:212555152..212557714-chr1:212585836..212588272,2	MCF-7	breast:
4	chr1:212554926..212556448-chr1:212559931..212561750,2	K562	blood:
5	chr1:212554525..212557472-chr1:212560250..212563380,3	K562	blood:

Variant related genes	Relation type
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1056985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863965	0.85[EUR][1000 genomes]
rs11119907	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11119908	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119910	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119918	0.96[ASN][1000 genomes]
rs11119927	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119932	0.85[EUR][1000 genomes]
rs11119934	0.85[EUR][1000 genomes]
rs12031941	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12033979	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118709	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118732	0.83[ASN][1000 genomes]
rs12119779	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12124582	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12128123	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128965	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12129267	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133582	0.85[EUR][1000 genomes]
rs12133636	0.99[ASN][1000 genomes]
rs12134074	0.83[ASN][1000 genomes]
rs12134599	1.00[ASN][1000 genomes]
rs12136095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137798	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12138533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12140158	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12141427	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12143853	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12145484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239580	0.86[ASN][1000 genomes]
rs12403586	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12561785	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12562618	0.83[ASN][1000 genomes]
rs1342152	0.81[ASN][1000 genomes]
rs1388033	0.85[EUR][1000 genomes]
rs1388034	0.85[EUR][1000 genomes]
rs14123	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1493601	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1808986	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2166155	0.87[ASN][1000 genomes]
rs2236598	0.81[ASN][1000 genomes]
rs2298115	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3767867	0.90[ASN][1000 genomes]
rs3820513	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4338424	0.84[EUR][1000 genomes]
rs4548507	0.91[ASN][1000 genomes]
rs4951597	0.85[EUR][1000 genomes]
rs74138154	0.84[EUR][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
rs12145170	PPP2R5A	cis	Thyroid	GTEx
rs12145170	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
4	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
5	chr1:212529400-212562400	Strong transcription	Dnd41	blood
6	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:212532400-212560200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:212533400-212557000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:212534000-212558200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:212534000-212570200	Weak transcription	HSMM	muscle
11	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:212534600-212560000	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:212535000-212561400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:212535200-212560200	Weak transcription	Hela-S3	cervix
15	chr1:212536200-212561600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:212538000-212571000	Weak transcription	NH-A	brain
17	chr1:212538200-212559600	Weak transcription	Right Atrium	heart
18	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
19	chr1:212540600-212562600	Weak transcription	Osteobl	bone
20	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
21	chr1:212540800-212556800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:212542800-212561600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
24	chr1:212545000-212561000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:212546800-212560200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:212546800-212560400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:212547000-212562600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:212547000-212563400	Strong transcription	Fetal Thymus	thymus
29	chr1:212547200-212561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:212547400-212562400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:212547400-212562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:212548200-212560600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:212548600-212563800	Strong transcription	Primary T cells from cord blood	blood
34	chr1:212548800-212558800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:212549400-212560600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:212549400-212561000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr1:212549600-212560200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:212549800-212558600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:212550400-212561000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:212550400-212562800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:212551000-212557800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:212551400-212556600	Weak transcription	HSMMtube	muscle
43	chr1:212551400-212561800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:212551600-212558000	Weak transcription	NHLF	lung
45	chr1:212551600-212560000	Weak transcription	Colonic Mucosa	Colon
46	chr1:212552000-212557600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:212552000-212559600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:212552000-212562000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:212552200-212557200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:212552400-212557600	Weak transcription	Rectal Mucosa Donor 29	rectum

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