Variant report

Variant	rs4951580
Chromosome Location	chr1:212391954-212391955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1011232	0.87[CHB][hapmap]
rs1056985	0.93[CEU][hapmap]
rs10735509	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs10779573	0.82[AMR][1000 genomes]
rs10863955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863957	0.90[CHB][hapmap]
rs10863958	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs11119874	0.82[AMR][1000 genomes]
rs11119886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119888	0.90[CHB][hapmap]
rs11119890	0.87[CHB][hapmap]
rs11119891	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs11119910	0.81[CEU][hapmap]
rs12022111	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12119779	0.93[CEU][hapmap]
rs12124065	0.85[ASN][1000 genomes]
rs12127954	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs12128965	0.93[CEU][hapmap]
rs12133134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12135257	0.83[AMR][1000 genomes]
rs12136095	0.93[CEU][hapmap]
rs12136808	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12137322	0.80[AMR][1000 genomes]
rs12141427	0.93[CEU][hapmap]
rs12142929	0.83[AMR][1000 genomes]
rs12143853	1.00[CEU][hapmap]
rs12145030	0.80[AMR][1000 genomes]
rs12145377	0.83[CEU][hapmap]
rs12145484	0.93[CEU][hapmap]
rs12403586	0.93[CEU][hapmap]
rs12407827	0.82[AMR][1000 genomes]
rs1342152	0.93[CEU][hapmap]
rs14123	0.93[CEU][hapmap]
rs1493602	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17018685	0.82[AMR][1000 genomes]
rs17018777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17018847	0.92[CEU][hapmap]
rs17018853	0.92[CEU][hapmap]
rs17663598	0.82[EUR][1000 genomes]
rs2358446	0.83[EUR][1000 genomes]
rs3820513	0.93[CEU][hapmap]
rs399429	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4418675	0.82[AMR][1000 genomes]
rs4951446	1.00[AFR][1000 genomes]
rs4951575	0.80[AMR][1000 genomes]
rs884923	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903119	0.93[CEU][hapmap]
rs9793334	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9793974	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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
rs4951580	PPP2R5A	cis	Whole Blood	GTEx
rs4951580	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212383000-212393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:212383400-212394600	Weak transcription	Left Ventricle	heart
3	chr1:212388600-212392400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:212388600-212393000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:212388600-212393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:212389000-212392000	Weak transcription	K562	blood
7	chr1:212389000-212393000	Weak transcription	Fetal Intestine Large	intestine
8	chr1:212390800-212392600	Enhancers	Adipose Nuclei	Adipose
9	chr1:212390800-212393800	Enhancers	Fetal Heart	heart
10	chr1:212391000-212392000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:212391000-212392200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:212391000-212392200	Enhancers	Fetal Intestine Small	intestine
13	chr1:212391000-212392200	Enhancers	Fetal Muscle Leg	muscle
14	chr1:212391000-212392200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:212391000-212392400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:212391000-212392600	Enhancers	HUVEC	blood vessel
17	chr1:212391000-212393400	Enhancers	Stomach Mucosa	stomach
18	chr1:212391000-212393800	Enhancers	Fetal Thymus	thymus
19	chr1:212391000-212393800	Enhancers	Thymus	Thymus
20	chr1:212391000-212393800	Enhancers	NHDF-Ad	bronchial
21	chr1:212391200-212392000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:212391200-212392200	Enhancers	Right Atrium	heart
23	chr1:212391200-212392200	Bivalent Enhancer	HepG2	liver
24	chr1:212391200-212392400	Enhancers	Gastric	stomach
25	chr1:212391200-212392600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr1:212391200-212392600	Enhancers	Spleen	Spleen
27	chr1:212391200-212392800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:212391200-212393000	Weak transcription	Placenta	Placenta
29	chr1:212391200-212393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:212391200-212393800	Enhancers	HSMMtube	muscle
31	chr1:212391200-212394000	Enhancers	Fetal Kidney	kidney
32	chr1:212391200-212394000	Enhancers	Fetal Lung	lung
33	chr1:212391200-212399000	Weak transcription	Pancreas	Pancrea
34	chr1:212391400-212392400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:212391400-212392600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:212391600-212392000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:212391600-212392200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:212391600-212392800	Enhancers	Osteobl	bone
39	chr1:212391600-212393400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:212391600-212393600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:212391600-212393800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:212391800-212392000	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr1:212391800-212392000	Enhancers	Small Intestine	intestine
44	chr1:212391800-212392200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:212391800-212392200	Flanking Active TSS	GM12878-XiMat	blood
46	chr1:212391800-212392400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:212391800-212392600	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:212391800-212392600	Enhancers	Dnd41	blood
49	chr1:212391800-212393200	Enhancers	Primary T cells from cord blood	blood
50	chr1:212391800-212393400	Weak transcription	Lung	lung

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