Variant report

Variant	rs348937
Chromosome Location	chr5:112825677-112825678
allele	A/G
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	CBX3	chr5:112824784-112825698	HCT-116	colon:	n/a	n/a
2	FOSL1	chr5:112824934-112825697	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
3	CEBPB	chr5:112824567-112825739	HCT-116	colon:	n/a	n/a
4	TCF12	chr5:112824885-112825690	SK-N-SH	brain:	n/a	n/a
5	JUND	chr5:112823928-112825693	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
6	FOSL1	chr5:112823968-112825681	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
7	CEBPB	chr5:112825010-112825691	IMR90	lung:	n/a	n/a
8	RCOR1	chr5:112822825-112826281	IMR90	lung:	n/a	n/a
9	SETDB1	chr5:112825034-112826408	K562	blood:	n/a	n/a
10	MAZ	chr5:112823544-112826068	IMR90	lung:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
11	CBX3	chr5:112823731-112825907	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
MCC	TF binding region
RNU4ATAC13P	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10035293	0.95[YRI][hapmap]
rs10038504	0.95[YRI][hapmap]
rs10043783	0.91[YRI][hapmap]
rs10043834	0.95[YRI][hapmap]
rs10053052	0.91[YRI][hapmap]
rs10053157	0.91[YRI][hapmap]
rs10053622	0.95[YRI][hapmap]
rs10055327	0.91[YRI][hapmap]
rs10057264	0.91[YRI][hapmap]
rs10066163	0.87[YRI][hapmap]
rs11952758	0.91[YRI][hapmap]
rs11960559	0.95[YRI][hapmap]
rs164253	0.80[CEU][hapmap]
rs17135618	0.95[YRI][hapmap]
rs2416282	0.83[GIH][hapmap]
rs348943	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3857436	0.95[YRI][hapmap]
rs485210	0.87[GIH][hapmap]
rs6879177	0.95[YRI][hapmap]
rs6879370	0.95[YRI][hapmap]
rs7709550	0.91[YRI][hapmap]
rs7709818	0.91[YRI][hapmap]
rs7722421	0.91[YRI][hapmap]
rs7731451	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs348937	YTHDC2	cis	cerebellum	SCAN
rs348937	DCP2	cis	parietal	SCAN
rs348937	YTHDC2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112823800-112826800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
2	chr5:112824400-112825800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:112824400-112825800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
4	chr5:112824600-112825800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:112824600-112826000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:112824600-112826000	Enhancers	Dnd41	blood
7	chr5:112824800-112825800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:112824800-112826000	Enhancers	NHLF	lung
9	chr5:112825000-112825800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:112825000-112825800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:112825000-112826000	Enhancers	HMEC	breast
12	chr5:112825000-112826000	Enhancers	NHEK	skin
13	chr5:112825200-112825800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:112825200-112825800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
15	chr5:112825200-112825800	Enhancers	NHDF-Ad	bronchial
16	chr5:112825200-112825800	Enhancers	Osteobl	bone
17	chr5:112825400-112825800	Flanking Active TSS	HSMMtube	muscle
18	chr5:112825400-112827600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr5:112825600-112825800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:112825600-112825800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:112825600-112825800	Enhancers	NH-A	brain
22	chr5:112825600-112826000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:112825600-112826000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:112825600-112826000	Enhancers	HSMM	muscle
25	chr5:112825600-112828200	Weak transcription	Aorta	Aorta

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