Variant report

Variant	rs3212418
Chromosome Location	chr5:52316172-52316173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52283546..52286213-chr5:52315102..52316776,2	MCF-7	breast:
2	chr5:52243837..52246026-chr5:52316094..52318313,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1421942	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3212391	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3212521	0.87[YRI][hapmap]
rs35235	0.81[GIH][hapmap];0.80[MEX][hapmap]
rs4865756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450106	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	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
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3212418	ITGA2	cis	Artery Tibial	GTEx
rs3212418	ESM1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52303400-52320400	Weak transcription	Fetal Brain Male	brain
2	chr5:52305200-52317200	Weak transcription	A549	lung
3	chr5:52307000-52333800	Weak transcription	Gastric	stomach
4	chr5:52311800-52317200	Weak transcription	NHLF	lung
5	chr5:52312000-52318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52313400-52319400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:52313600-52318400	Weak transcription	NHDF-Ad	bronchial
8	chr5:52313600-52319800	Weak transcription	NH-A	brain
9	chr5:52313600-52321000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:52313800-52318800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:52313800-52319800	Weak transcription	Brain Angular Gyrus	brain
12	chr5:52313800-52320400	Weak transcription	Brain Anterior Caudate	brain
13	chr5:52313800-52323400	Weak transcription	Spleen	Spleen
14	chr5:52314200-52316400	Enhancers	HepG2	liver
15	chr5:52314200-52317400	Weak transcription	Brain Substantia Nigra	brain
16	chr5:52314200-52319600	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:52314200-52328600	Weak transcription	Lung	lung
18	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:52314400-52316400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:52314400-52317200	Weak transcription	NHEK	skin
21	chr5:52314400-52323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:52314400-52323400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:52314400-52326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:52314600-52316200	Enhancers	HUVEC	blood vessel
25	chr5:52314800-52317200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:52315400-52316400	Enhancers	HMEC	breast
27	chr5:52315600-52317200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:52315600-52317200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:52315600-52317200	Weak transcription	Hela-S3	cervix
30	chr5:52315600-52317400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:52315800-52316200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:52315800-52317600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:52316000-52316400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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