Variant report

Variant	rs4318523
Chromosome Location	chr3:145616862-145616863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145604775..145606383-chr3:145616815..145618517,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10935589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711135	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711136	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11714711	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719451	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12491155	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632142	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061647	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13073973	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13091194	0.91[ASN][1000 genomes]
rs1355788	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355789	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513404	0.82[ASN][1000 genomes]
rs1513423	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1522331	0.91[ASN][1000 genomes]
rs1967207	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036469	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036470	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34309398	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34906476	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3914310	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3914311	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67122199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633606	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9790074	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	esv2757015	chr3:145615852-145661771	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv2759186	chr3:145615852-145661771	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4318523	PLSCR2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145615000-145621000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:145615800-145617000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:145615800-145617000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:145615800-145617200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:145615800-145617400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:145615800-145617400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:145616000-145617000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:145616000-145617600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:145616200-145617000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:145616200-145617000	Enhancers	Adipose Nuclei	Adipose
11	chr3:145616200-145617000	Active TSS	Stomach Smooth Muscle	stomach
12	chr3:145616200-145617000	Flanking Active TSS	Hela-S3	cervix
13	chr3:145616400-145617000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:145616400-145617000	Active TSS	Colon Smooth Muscle	Colon
15	chr3:145616600-145617000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr3:145616600-145617000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:145616600-145617000	Enhancers	NH-A	brain
18	chr3:145616600-145617000	Enhancers	NHDF-Ad	bronchial
19	chr3:145616600-145617200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:145616600-145617400	Enhancers	HSMMtube	muscle
21	chr3:145616600-145618200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:145616600-145621000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:145616800-145617000	Enhancers	Osteobl	bone
24	chr3:145616800-145617200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:145616800-145617200	Enhancers	Pancreatic Islets	Pancreatic Islet

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