Variant report

Variant	rs12145377
Chromosome Location	chr1:212432926-212432927
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212428170..212430153-chr1:212432529..212434264,2	K562	blood:
2	chr1:212427899..212432292-chr1:212432529..212438731,7	K562	blood:
3	chr1:212432823..212434470-chr1:212457491..212460083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1011232	0.82[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1056985	0.92[CEU][hapmap]
rs10735509	0.83[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10779577	0.97[ASN][1000 genomes]
rs10863955	0.83[CEU][hapmap]
rs10863956	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863957	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10863958	0.83[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10863965	0.92[CEU][hapmap]
rs11119886	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs11119888	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11119890	0.92[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11119891	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119903	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11119910	0.90[CEU][hapmap]
rs11119932	0.92[CEU][hapmap]
rs11119934	0.83[CEU][hapmap]
rs12118732	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12119183	0.92[ASN][1000 genomes]
rs12119779	0.92[CEU][hapmap]
rs12124582	0.85[AMR][1000 genomes]
rs12127954	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12128965	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs12133582	0.92[CEU][hapmap]
rs12134074	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12136095	0.92[CEU][hapmap]
rs12141427	0.92[CEU][hapmap]
rs12143853	0.89[CEU][hapmap]
rs12145451	0.97[ASN][1000 genomes]
rs12145484	0.92[CEU][hapmap]
rs12146141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12403586	0.92[CEU][hapmap]
rs12562618	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1342152	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs14123	0.92[CEU][hapmap]
rs1493601	0.85[AMR][1000 genomes]
rs17018777	0.83[CEU][hapmap]
rs17018847	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17018853	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820513	0.92[CEU][hapmap]
rs4951597	0.92[CEU][hapmap]
rs61260530	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884923	0.82[EUR][1000 genomes]
rs903119	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs12145377	PPP2R5A	cis	Thyroid	GTEx
rs12145377	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212428600-212434000	Weak transcription	Esophagus	oesophagus
2	chr1:212428800-212434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:212429200-212434200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:212429200-212434400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:212429400-212434000	Weak transcription	Stomach Mucosa	stomach
6	chr1:212429400-212434800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:212429400-212435600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:212429600-212433000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:212429600-212434000	Weak transcription	Fetal Intestine Large	intestine
10	chr1:212429600-212434200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:212429800-212434000	Weak transcription	K562	blood
12	chr1:212430000-212433600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:212430000-212433800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:212430200-212433200	Enhancers	Primary T cells from cord blood	blood
15	chr1:212430200-212434600	Weak transcription	Left Ventricle	heart
16	chr1:212430400-212435600	Enhancers	HepG2	liver
17	chr1:212430600-212434000	Weak transcription	Lung	lung
18	chr1:212430600-212435000	Enhancers	Adipose Nuclei	Adipose
19	chr1:212430800-212434000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:212430800-212434400	Weak transcription	Right Atrium	heart
21	chr1:212430800-212434400	Weak transcription	Right Ventricle	heart
22	chr1:212431000-212434000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr1:212431000-212434200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:212431200-212434000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:212431600-212433600	Weak transcription	Liver	Liver
26	chr1:212431800-212433600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:212431800-212433800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:212431800-212433800	Weak transcription	Small Intestine	intestine
29	chr1:212431800-212434000	Weak transcription	Pancreas	Pancrea
30	chr1:212431800-212434200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:212431800-212434400	Weak transcription	Gastric	stomach
32	chr1:212432000-212433200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:212432200-212433000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:212432400-212433600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:212432800-212433000	Enhancers	Primary B cells from cord blood	blood
36	chr1:212432800-212434000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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