Variant report

Variant	rs10863955
Chromosome Location	chr1:212401103-212401104
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1011232	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs1056985	0.93[CEU][hapmap]
rs10735509	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10863957	0.85[CHB][hapmap]
rs10863958	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10863965	0.93[CEU][hapmap]
rs11119886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119888	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11119890	0.82[CHB][hapmap]
rs11119891	0.93[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs11119910	0.82[CEU][hapmap]
rs11119932	0.93[CEU][hapmap]
rs11119941	1.00[AFR][1000 genomes]
rs12022111	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12119779	0.93[CEU][hapmap]
rs12124065	0.85[ASN][1000 genomes]
rs12127954	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs12128965	0.93[CEU][hapmap]
rs12133134	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12136095	0.93[CEU][hapmap]
rs12136808	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12141427	0.93[CEU][hapmap]
rs12143853	1.00[CEU][hapmap]
rs12145377	0.83[CEU][hapmap]
rs12145484	0.93[CEU][hapmap]
rs12403586	0.93[CEU][hapmap]
rs1342152	0.93[CEU][hapmap]
rs14123	0.93[CEU][hapmap]
rs1493602	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17018777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17018847	0.92[CEU][hapmap]
rs17018853	0.92[CEU][hapmap]
rs3820513	0.93[CEU][hapmap]
rs399429	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951446	1.00[AFR][1000 genomes]
rs4951447	1.00[AFR][1000 genomes]
rs4951580	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951597	0.93[CEU][hapmap]
rs4951598	1.00[AFR][1000 genomes]
rs4951600	1.00[AFR][1000 genomes]
rs884923	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903119	0.93[CEU][hapmap]
rs9793334	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9793974	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10863955	PPP2R5A	cis	Whole Blood	GTEx
rs10863955	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212392600-212404800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:212398000-212402000	Enhancers	HepG2	liver
3	chr1:212398600-212402000	Enhancers	Liver	Liver
4	chr1:212398800-212402600	Enhancers	Stomach Mucosa	stomach
5	chr1:212399000-212403200	Enhancers	Fetal Heart	heart
6	chr1:212399400-212401600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:212399400-212401800	Weak transcription	Fetal Lung	lung
8	chr1:212399400-212405200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:212399600-212403200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:212399600-212404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:212399600-212404800	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:212399800-212401600	Weak transcription	Fetal Kidney	kidney
13	chr1:212399800-212401600	Weak transcription	Left Ventricle	heart
14	chr1:212399800-212403200	Weak transcription	Right Ventricle	heart
15	chr1:212399800-212403800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:212399800-212405200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:212399800-212406600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:212399800-212407800	Weak transcription	Brain Anterior Caudate	brain
19	chr1:212400000-212404800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:212400000-212405000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:212400000-212405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:212400000-212405200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:212400000-212405200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:212400000-212405200	Weak transcription	Fetal Thymus	thymus
25	chr1:212400000-212407600	Weak transcription	Spleen	Spleen
26	chr1:212400000-212407800	Weak transcription	Right Atrium	heart
27	chr1:212400000-212407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:212400200-212405400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:212400200-212406800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:212400600-212404200	Enhancers	Pancreas	Pancrea
31	chr1:212400800-212402800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:212401000-212401400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:212401000-212401400	Enhancers	Lung	lung
34	chr1:212401000-212401400	Enhancers	Small Intestine	intestine
35	chr1:212401000-212401800	Enhancers	Gastric	stomach
36	chr1:212401000-212402400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:212401000-212402600	Enhancers	NHDF-Ad	bronchial

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