Variant report

Variant	rs1522331
Chromosome Location	chr3:145583561-145583562
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10935589	0.91[ASN][1000 genomes]
rs10935590	0.82[AFR][1000 genomes]
rs11711135	0.88[ASN][1000 genomes]
rs11711136	0.88[ASN][1000 genomes]
rs11714711	0.88[ASN][1000 genomes]
rs11719451	0.92[ASN][1000 genomes]
rs12488991	0.83[YRI][hapmap]
rs12491155	0.91[ASN][1000 genomes]
rs12632142	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13061647	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13073973	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13074992	0.89[ASN][1000 genomes]
rs13091194	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355788	0.91[ASN][1000 genomes]
rs1355789	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1398776	0.81[ASW][hapmap];0.83[YRI][hapmap]
rs1398777	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1472665	0.91[ASN][1000 genomes]
rs1513404	0.91[ASN][1000 genomes]
rs1513423	0.90[ASN][1000 genomes]
rs1967207	0.91[ASN][1000 genomes]
rs2036469	0.91[ASN][1000 genomes]
rs2036470	0.90[ASN][1000 genomes]
rs34309398	0.90[ASN][1000 genomes]
rs34906476	0.90[ASN][1000 genomes]
rs35225711	0.90[AFR][1000 genomes]
rs3914310	0.91[ASN][1000 genomes]
rs3914311	0.91[ASN][1000 genomes]
rs4318523	0.91[ASN][1000 genomes]
rs67122199	0.91[ASN][1000 genomes]
rs7628962	0.90[AFR][1000 genomes]
rs7633606	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9790074	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3330499	chr3:145334189-145596853	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3379945	chr3:145351163-145679850	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877610	chr3:145465395-145653627	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2751980	chr3:145473020-145758194	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1013475	chr3:145478985-145750509	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1010509	chr3:145478985-145757483	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005624	chr3:145486437-145750509	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv999344	chr3:145506353-145750883	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv536757	chr3:145506353-145750883	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv33307	chr3:145506383-145667833	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv877611	chr3:145525989-145653627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv877612	chr3:145542558-145653627	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv591936	chr3:145548718-145608291	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1522331	PLSCR2	cis	parietal	SCAN
rs1522331	WWTR1	cis	parietal	SCAN
rs1522331	CACNB4	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145581000-145583600	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr3:145582600-145587600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:145583200-145583600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:145583200-145583600	Enhancers	Brain Hippocampus Middle	brain
5	chr3:145583200-145583800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:145583200-145583800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:145583200-145583800	Enhancers	Fetal Brain Female	brain
8	chr3:145583200-145584000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:145583200-145584000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:145583400-145583600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:145583400-145583800	Enhancers	Colon Smooth Muscle	Colon
12	chr3:145583400-145583800	Enhancers	Fetal Lung	lung

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