Variant report

Variant	rs3212386
Chromosome Location	chr5:52289013-52289014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:52283218-52289712	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:52288932-52289170	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:52287570..52290507-chr5:52297245..52299058,2	MCF-7	breast:
2	chr5:52284537..52287438-chr5:52289001..52291401,4	MCF-7	breast:
3	chr5:52287901..52290762-chr5:52300870..52303377,2	MCF-7	breast:
4	chr5:52288695..52291271-chr5:52292952..52294743,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000249899	TF binding region
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10061730	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10071255	0.80[CEU][hapmap]
rs12523395	1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap]
rs1363188	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1421941	0.80[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs16880539	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs16880541	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs16880636	0.85[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1871184	0.90[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3212627	0.86[YRI][hapmap]
rs4865754	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs59811911	0.82[EUR][1000 genomes]
rs66789666	0.84[AFR][1000 genomes]
rs67217308	0.84[AFR][1000 genomes]
rs67835512	0.84[AFR][1000 genomes]
rs6883028	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7722066	0.87[YRI][hapmap]
rs9292003	0.84[CEU][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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52295400	Weak transcription	Pancreas	Pancrea
2	chr5:52286200-52300400	Weak transcription	Gastric	stomach
3	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
4	chr5:52286200-52313600	Weak transcription	Lung	lung
5	chr5:52286600-52289400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:52286600-52289400	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:52286600-52291000	Weak transcription	Esophagus	oesophagus
8	chr5:52286600-52292000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:52286600-52292600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:52286600-52293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
13	chr5:52286800-52290400	Transcr. at gene 5' and 3'	NHEK	skin
14	chr5:52286800-52294400	Weak transcription	Osteobl	bone
15	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:52287000-52291000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:52287000-52292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:52287000-52293000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:52287000-52293400	Weak transcription	Fetal Intestine Small	intestine
20	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:52287200-52292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:52287200-52293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:52287200-52293400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:52287200-52293600	Weak transcription	Fetal Kidney	kidney
25	chr5:52287400-52289600	Enhancers	Brain Hippocampus Middle	brain
26	chr5:52287600-52290800	Transcr. at gene 5' and 3'	HMEC	breast
27	chr5:52288000-52292400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
28	chr5:52288200-52289400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:52288200-52289600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:52288200-52289800	Transcr. at gene 5' and 3'	HepG2	liver
31	chr5:52288200-52290000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:52288200-52290200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:52288200-52290400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:52288400-52289400	Genic enhancers	HUVEC	blood vessel
35	chr5:52288400-52290000	Strong transcription	NH-A	brain
36	chr5:52288600-52290000	Genic enhancers	NHLF	lung
37	chr5:52288800-52290800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:52288800-52290800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:52288800-52292000	Enhancers	NHDF-Ad	bronchial
40	chr5:52289000-52289200	Enhancers	Brain Angular Gyrus	brain
41	chr5:52289000-52289200	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr5:52289000-52289200	Strong transcription	A549	lung
43	chr5:52289000-52289400	Transcr. at gene 5' and 3'	Hela-S3	cervix
44	chr5:52289000-52290800	Enhancers	Brain Substantia Nigra	brain
45	chr5:52289000-52291600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain

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