Variant report

Variant	rs953239
Chromosome Location	chr3:142446205-142446206
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142442816..142444880-chr3:142445046..142446610,2	K562	blood:
2	chr3:142443512..142446497-chr3:142575988..142578278,2	K562	blood:
3	chr3:142296594..142299227-chr3:142445379..142447905,3	K562	blood:
4	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:

Variant related genes	Relation type
ENSG00000120756	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11715459	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11717993	0.87[ASN][1000 genomes]
rs11915805	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1604	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2049328	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2354856	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs28571594	0.86[AMR][1000 genomes]
rs28658009	0.87[ASN][1000 genomes]
rs34445140	0.87[ASN][1000 genomes]
rs35467195	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35862982	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821647	0.88[CHB][hapmap]
rs4259003	0.94[CHB][hapmap]
rs4530572	0.95[ASN][1000 genomes]
rs4539980	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55722370	0.87[ASN][1000 genomes]
rs55722917	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56666685	0.82[ASN][1000 genomes]
rs56775607	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57026466	0.87[ASN][1000 genomes]
rs60294656	0.87[ASN][1000 genomes]
rs60319320	0.87[ASN][1000 genomes]
rs60752859	0.87[ASN][1000 genomes]
rs6440104	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs6440106	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440107	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66897945	0.87[ASN][1000 genomes]
rs6777466	0.87[ASN][1000 genomes]
rs6784998	0.96[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6790959	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6798849	0.87[ASN][1000 genomes]
rs73232711	0.82[ASN][1000 genomes]
rs7623762	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs7623977	0.87[ASN][1000 genomes]
rs7626908	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7628728	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7629129	0.83[AMR][1000 genomes]
rs7631245	0.88[CHB][hapmap]
rs7635768	0.91[ASN][1000 genomes]
rs7637826	0.91[ASN][1000 genomes]
rs7637846	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs7641514	0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7642332	0.87[ASN][1000 genomes]
rs7644704	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7646197	0.87[ASN][1000 genomes]
rs7647291	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs953641	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs9758429	0.87[ASN][1000 genomes]
rs9815607	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs9820721	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9823836	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9861598	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9865053	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9868886	0.88[CHB][hapmap];0.86[JPT][hapmap]

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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs953239	PLS1	cis	cerebellum	SCAN
rs953239	ZIC1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142444000-142452600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:142444200-142467400	Weak transcription	HSMM	muscle
3	chr3:142444400-142446400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:142444400-142451000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:142444400-142451200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:142444400-142454400	Weak transcription	Ovary	ovary
7	chr3:142444400-142467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:142444400-142469600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:142444600-142451200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:142444600-142453800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:142444600-142454200	Weak transcription	NHLF	lung
12	chr3:142444600-142467200	Weak transcription	NH-A	brain
13	chr3:142445000-142446400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:142445000-142446400	Enhancers	HepG2	liver
15	chr3:142445000-142451000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:142445000-142451200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:142445000-142467400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:142445000-142467800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:142445000-142479000	Weak transcription	Fetal Brain Female	brain
20	chr3:142445200-142447800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:142445200-142449000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:142445200-142450800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:142445200-142451000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:142445200-142467000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:142445200-142467000	Weak transcription	NHDF-Ad	bronchial
26	chr3:142445200-142467000	Weak transcription	Osteobl	bone
27	chr3:142445200-142467200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:142445200-142467400	Weak transcription	HMEC	breast
29	chr3:142445400-142467200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:142445600-142450600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:142445800-142447600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:142445800-142467400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:142446000-142446400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:142446000-142467000	Weak transcription	A549	lung
35	chr3:142446200-142447000	Enhancers	K562	blood
36	chr3:142446200-142448000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links