Variant report

Variant	rs17018777
Chromosome Location	chr1:212394364-212394365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212389745..212391730-chr1:212393335..212395896,2	K562	blood:
2	chr1:212393346..212396328-chr1:212457940..212460726,2	K562	blood:
3	chr1:212391958..212394846-chr1:212458658..212460726,2	K562	blood:
4	chr1:212325848..212328405-chr1:212392780..212395278,2	K562	blood:

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:47)

rs_ID	r²[population]
rs1011232	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1056985	0.93[CEU][hapmap]
rs10735509	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10779573	0.80[AMR][1000 genomes]
rs10863955	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]
rs10863957	0.86[CHB][hapmap]
rs10863958	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11119874	0.80[AMR][1000 genomes]
rs11119886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119888	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11119890	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11119891	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11119910	0.82[CEU][hapmap]
rs11119941	1.00[AFR][1000 genomes]
rs12022111	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12119779	0.93[CEU][hapmap]
rs12124065	0.85[ASN][1000 genomes]
rs12127954	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12128965	0.93[CEU][hapmap]
rs12133134	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs12135257	0.82[AMR][1000 genomes]
rs12136095	0.93[CEU][hapmap]
rs12136808	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12141427	0.93[CEU][hapmap]
rs12142929	0.82[AMR][1000 genomes]
rs12143853	1.00[CEU][hapmap]
rs12145377	0.83[CEU][hapmap]
rs12145484	0.93[CEU][hapmap]
rs12403586	0.93[CEU][hapmap]
rs12407827	0.80[AMR][1000 genomes]
rs1342152	0.93[CEU][hapmap]
rs14123	0.93[CEU][hapmap]
rs1493602	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17018685	0.80[AMR][1000 genomes]
rs17018847	0.92[CEU][hapmap]
rs17018853	0.92[CEU][hapmap]
rs2358446	0.80[EUR][1000 genomes]
rs3820513	0.93[CEU][hapmap]
rs399429	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4418675	0.80[AMR][1000 genomes]
rs4951446	1.00[AFR][1000 genomes]
rs4951447	1.00[AFR][1000 genomes]
rs4951580	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884923	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903119	0.93[CEU][hapmap]
rs9793334	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9793974	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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
rs17018777	PPP2R5A	cis	Whole Blood	GTEx
rs17018777	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212383400-212394600	Weak transcription	Left Ventricle	heart
2	chr1:212391200-212399000	Weak transcription	Pancreas	Pancrea
3	chr1:212392000-212396000	Enhancers	K562	blood
4	chr1:212392000-212399400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:212392200-212395200	Weak transcription	Right Atrium	heart
6	chr1:212392200-212398600	Weak transcription	Right Ventricle	heart
7	chr1:212392200-212399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:212392200-212399200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:212392400-212394400	Weak transcription	Gastric	stomach
10	chr1:212392400-212397800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:212392400-212398600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:212392600-212397400	Weak transcription	Adipose Nuclei	Adipose
13	chr1:212392600-212399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:212392600-212399200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:212392600-212404800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:212393000-212395400	Enhancers	Spleen	Spleen
17	chr1:212393200-212398600	Weak transcription	Primary T cells from cord blood	blood
18	chr1:212393400-212395600	Enhancers	Lung	lung
19	chr1:212393400-212398800	Weak transcription	Stomach Mucosa	stomach
20	chr1:212393600-212394800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:212393600-212395000	Weak transcription	Placenta	Placenta
22	chr1:212393600-212398600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:212393600-212398600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:212393600-212398800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:212393600-212398800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:212393600-212399200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:212393600-212399200	Weak transcription	Small Intestine	intestine
28	chr1:212393800-212394600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:212393800-212394600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:212393800-212395200	Weak transcription	HSMMtube	muscle
31	chr1:212393800-212395200	Weak transcription	NHDF-Ad	bronchial
32	chr1:212393800-212398200	Weak transcription	Fetal Thymus	thymus
33	chr1:212393800-212398600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:212393800-212399000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:212393800-212399000	Weak transcription	Fetal Heart	heart
36	chr1:212394000-212394400	Weak transcription	Fetal Lung	lung
37	chr1:212394000-212394600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:212394000-212395000	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links