Variant report

Variant	rs884923
Chromosome Location	chr1:212406616-212406617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212406214..212407731-chr1:212435193..212437929,2	K562	blood:
2	chr1:212404851..212407731-chr1:212434475..212437929,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1011232	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1056985	0.92[CEU][hapmap]
rs10735509	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10863955	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863956	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10863957	0.80[CHB][hapmap]
rs10863958	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10863965	0.92[CEU][hapmap]
rs11119886	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119888	0.80[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11119890	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11119891	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11119893	0.82[EUR][1000 genomes]
rs11119910	0.82[CEU][hapmap]
rs11119932	0.92[CEU][hapmap]
rs11119934	0.84[CEU][hapmap]
rs12022111	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12119779	0.92[CEU][hapmap]
rs12124065	0.84[ASN][1000 genomes]
rs12127954	0.81[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs12128965	0.92[CEU][hapmap]
rs12133134	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12133582	0.92[CEU][hapmap]
rs12136095	0.92[CEU][hapmap]
rs12136808	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12141427	0.92[CEU][hapmap]
rs12143853	1.00[CEU][hapmap]
rs12145377	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12145484	0.92[CEU][hapmap]
rs12146141	0.82[EUR][1000 genomes]
rs12403586	0.92[CEU][hapmap]
rs1342152	0.92[CEU][hapmap]
rs14123	0.92[CEU][hapmap]
rs1493602	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17018777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17018847	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs17018853	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs3820513	0.92[CEU][hapmap]
rs399429	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4951580	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951597	0.92[CEU][hapmap]
rs903119	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs9793334	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9793974	0.84[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs884923	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212399800-212407800	Weak transcription	Brain Anterior Caudate	brain
2	chr1:212400000-212407600	Weak transcription	Spleen	Spleen
3	chr1:212400000-212407800	Weak transcription	Right Atrium	heart
4	chr1:212400000-212407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:212400200-212406800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:212401400-212408400	Weak transcription	Lung	lung
7	chr1:212401800-212409000	Weak transcription	Gastric	stomach
8	chr1:212402400-212407800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:212403400-212409000	Weak transcription	Fetal Intestine Large	intestine
10	chr1:212403600-212407000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:212403600-212407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:212403600-212408200	Weak transcription	Small Intestine	intestine
13	chr1:212403600-212409600	Weak transcription	Liver	Liver
14	chr1:212403800-212407600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:212403800-212407600	Weak transcription	NHDF-Ad	bronchial
16	chr1:212403800-212407600	Weak transcription	Osteobl	bone
17	chr1:212404000-212407200	Weak transcription	Right Ventricle	heart
18	chr1:212404600-212407800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:212404800-212410800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:212405000-212406800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:212405200-212407600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:212405200-212408800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:212405200-212410600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:212405600-212406800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:212405600-212406800	Weak transcription	GM12878-XiMat	blood
26	chr1:212405600-212407000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:212405600-212407000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:212405600-212407200	Weak transcription	Left Ventricle	heart
29	chr1:212405600-212407600	Weak transcription	Psoas Muscle	Psoas
30	chr1:212405600-212408600	Weak transcription	Pancreas	Pancrea
31	chr1:212405600-212409000	Weak transcription	Esophagus	oesophagus
32	chr1:212405600-212414800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:212405600-212416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:212405800-212406800	Weak transcription	Stomach Mucosa	stomach
35	chr1:212405800-212406800	Weak transcription	K562	blood
36	chr1:212405800-212407800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:212405800-212408000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:212406000-212407800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:212406200-212407000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:212406400-212407000	Enhancers	Fetal Heart	heart
41	chr1:212406400-212407600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:212406400-212408000	Enhancers	Fetal Muscle Trunk	muscle
43	chr1:212406400-212411000	Enhancers	HSMMtube	muscle
44	chr1:212406600-212406800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:212406600-212407000	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr1:212406600-212409200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:212406600-212410800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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