Variant report

Variant	rs12141427
Chromosome Location	chr1:212562252-212562253
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212561364..212563303-chr1:212611566..212613873,2	K562	blood:
2	chr1:212554525..212557472-chr1:212560250..212563380,3	K562	blood:
3	chr1:212559670..212562304-chr1:212569400..212571450,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1056985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863955	0.93[CEU][hapmap]
rs10863965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119886	0.93[CEU][hapmap]
rs11119891	1.00[CEU][hapmap]
rs11119907	0.82[EUR][1000 genomes]
rs11119908	0.82[EUR][1000 genomes]
rs11119910	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11119918	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11119927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119934	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12031941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12033979	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118709	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12119779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128123	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12128965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs12129267	0.82[EUR][1000 genomes]
rs12133582	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133636	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs12134599	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12136095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12137798	0.82[EUR][1000 genomes]
rs12138533	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140158	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12143853	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12145170	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12145377	0.92[CEU][hapmap]
rs12145484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12239580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12403586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12561785	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1342152	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1388033	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1388034	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs14123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17018777	0.93[CEU][hapmap]
rs17018847	1.00[CEU][hapmap]
rs17018853	1.00[CEU][hapmap]
rs17666015	0.83[EUR][1000 genomes]
rs1808986	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2298115	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs3754142	0.83[CHB][hapmap]
rs3754144	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3767867	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3767868	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3767872	0.83[AFR][1000 genomes]
rs3820513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4338424	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4548507	1.00[ASN][1000 genomes]
rs4951596	0.87[ASN][1000 genomes]
rs4951597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59001230	0.83[AFR][1000 genomes]
rs74138154	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs765364	0.82[JPT][hapmap]
rs903119	1.00[CEU][hapmap]

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
rs12141427	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	chr1:212502600-212563400	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	chr1:212534000-212570200	Weak transcription	HSMM	muscle
8	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:212538000-212571000	Weak transcription	NH-A	brain
10	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
11	chr1:212540600-212562600	Weak transcription	Osteobl	bone
12	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
13	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
14	chr1:212547000-212562600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:212547000-212563400	Strong transcription	Fetal Thymus	thymus
16	chr1:212547400-212562400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:212547400-212562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:212548600-212563800	Strong transcription	Primary T cells from cord blood	blood
19	chr1:212550400-212562800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:212553000-212562600	Strong transcription	GM12878-XiMat	blood
21	chr1:212553200-212569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:212553200-212578400	Weak transcription	K562	blood
23	chr1:212554600-212562400	Strong transcription	Thymus	Thymus
24	chr1:212554800-212562400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:212554800-212562600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:212555400-212563200	Weak transcription	Psoas Muscle	Psoas
27	chr1:212555600-212562600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:212556600-212562800	Strong transcription	Primary B cells from cord blood	blood
29	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
30	chr1:212558000-212562400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:212558600-212578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:212558600-212580000	Weak transcription	Left Ventricle	heart
33	chr1:212559000-212562400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:212559200-212564800	Weak transcription	HMEC	breast
35	chr1:212559400-212563600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:212560000-212562600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:212560000-212562800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:212560200-212563200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:212560200-212578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:212560400-212562400	Weak transcription	Colonic Mucosa	Colon
41	chr1:212560400-212562800	Weak transcription	Brain Angular Gyrus	brain
42	chr1:212560400-212563200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:212560400-212570600	Weak transcription	NHLF	lung
44	chr1:212560400-212580200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:212560600-212562400	Weak transcription	Placenta	Placenta
46	chr1:212560600-212562600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:212560600-212562600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:212560600-212562600	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:212560600-212562600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:212560600-212562800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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