Variant report

Variant	rs1345128
Chromosome Location	chr2:47006474-47006475
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47005678..47008315-chr2:47011541..47013639,2	MCF-7	breast:
2	chr2:46872190..46873901-chr2:47005919..47008590,2	K562	blood:
3	chr2:46881672..46884638-chr2:47005149..47007963,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SOCS5-1	chr2:47004922-47007384	ENSG00000260977.1

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1009231	0.85[YRI][hapmap]
rs10168342	0.85[YRI][hapmap]
rs1456009	0.85[YRI][hapmap]
rs4522653	0.85[YRI][hapmap]
rs6740539	0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6746471	0.85[YRI][hapmap]
rs6748938	0.85[YRI][hapmap]
rs6756738	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs897528	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1345128	PIGF	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46981400-47006800	Weak transcription	Psoas Muscle	Psoas
2	chr2:46985600-47008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:47001000-47008600	Enhancers	Osteobl	bone
4	chr2:47002800-47007000	Weak transcription	Ovary	ovary
5	chr2:47004000-47006600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:47005000-47008600	Enhancers	HepG2	liver
7	chr2:47005200-47009400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:47005200-47010000	Enhancers	Fetal Lung	lung
9	chr2:47005400-47009200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:47005400-47009200	Enhancers	NHLF	lung
11	chr2:47005400-47009400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:47005400-47012400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:47005600-47007000	Enhancers	NHEK	skin
14	chr2:47005600-47008200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:47005600-47008200	Enhancers	HMEC	breast
16	chr2:47005600-47009400	Enhancers	Fetal Heart	heart
17	chr2:47005600-47009400	Enhancers	NHDF-Ad	bronchial
18	chr2:47005600-47010000	Enhancers	Left Ventricle	heart
19	chr2:47005800-47006600	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:47005800-47007400	Enhancers	Hela-S3	cervix
21	chr2:47005800-47008200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:47005800-47008200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:47005800-47008400	Enhancers	NH-A	brain
24	chr2:47005800-47009000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:47005800-47009200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:47005800-47009800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:47006000-47006600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:47006000-47006600	Weak transcription	Lung	lung
29	chr2:47006000-47006800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:47006000-47007200	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:47006000-47007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:47006000-47008200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:47006000-47008400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:47006200-47006600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:47006200-47006600	Weak transcription	Right Atrium	heart
36	chr2:47006200-47007200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr2:47006200-47007400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:47006200-47007400	Weak transcription	Fetal Brain Male	brain
39	chr2:47006200-47008600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:47006400-47006600	Flanking Active TSS	A549	lung
41	chr2:47006400-47006800	Weak transcription	Pancreas	Pancrea
42	chr2:47006400-47006800	Enhancers	HSMMtube	muscle
43	chr2:47006400-47007000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:47006400-47007000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:47006400-47007200	Enhancers	HSMM	muscle
46	chr2:47006400-47008400	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:47006400-47009000	Enhancers	Stomach Mucosa	stomach
48	chr2:47006400-47009800	Enhancers	Fetal Stomach	stomach
49	chr2:47006400-47009800	Enhancers	Right Ventricle	heart

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