Variant report

Variant	rs3212657
Chromosome Location	chr5:52288482-52288483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:52288440-52288864	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:52283218-52289712	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52287570..52290507-chr5:52297245..52299058,2	MCF-7	breast:
2	chr5:52287901..52290762-chr5:52300870..52303377,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA1-1	chr5:52286944-52290794	ucscGeneNc_uc003jox_1

Variant related genes	Relation type
ENSG00000249899	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10461562	0.96[EUR][1000 genomes]
rs1363191	0.88[CEU][hapmap]
rs1445937	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16880627	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs2279584	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3212392	0.82[EUR][1000 genomes]
rs41315912	0.81[EUR][1000 genomes]
rs58231501	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867926	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7703474	0.81[EUR][1000 genomes]
rs7705061	0.81[EUR][1000 genomes]
rs9637769	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3212657	CCNO	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52289000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:52286200-52295400	Weak transcription	Pancreas	Pancrea
3	chr5:52286200-52300400	Weak transcription	Gastric	stomach
4	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
5	chr5:52286200-52313600	Weak transcription	Lung	lung
6	chr5:52286400-52289000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:52286600-52289400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:52286600-52289400	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:52286600-52291000	Weak transcription	Esophagus	oesophagus
10	chr5:52286600-52292000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:52286600-52292600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:52286600-52293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
15	chr5:52286800-52290400	Transcr. at gene 5' and 3'	NHEK	skin
16	chr5:52286800-52294400	Weak transcription	Osteobl	bone
17	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
18	chr5:52287000-52291000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:52287000-52292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:52287000-52293000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:52287000-52293400	Weak transcription	Fetal Intestine Small	intestine
22	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:52287200-52292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:52287200-52293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:52287200-52293400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:52287200-52293600	Weak transcription	Fetal Kidney	kidney
27	chr5:52287400-52289600	Enhancers	Brain Hippocampus Middle	brain
28	chr5:52287600-52290800	Transcr. at gene 5' and 3'	HMEC	breast
29	chr5:52287800-52288600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:52287800-52288800	Weak transcription	NHDF-Ad	bronchial
31	chr5:52288000-52288600	Transcr. at gene 5' and 3'	Hela-S3	cervix
32	chr5:52288000-52292400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
33	chr5:52288200-52288600	Transcr. at gene 5' and 3'	NHLF	lung
34	chr5:52288200-52288800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:52288200-52289400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:52288200-52289600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:52288200-52289800	Transcr. at gene 5' and 3'	HepG2	liver
38	chr5:52288200-52290000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:52288200-52290200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:52288200-52290400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:52288400-52288800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:52288400-52288800	Bivalent Enhancer	Brain Anterior Caudate	brain
43	chr5:52288400-52288800	Strong transcription	A549	lung
44	chr5:52288400-52289000	Genic enhancers	Brain Substantia Nigra	brain
45	chr5:52288400-52289400	Genic enhancers	HUVEC	blood vessel
46	chr5:52288400-52290000	Strong transcription	NH-A	brain

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