Variant report

Variant	rs12484015
Chromosome Location	chr22:33121330-33121331
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11089591	0.85[ASN][1000 genomes]
rs13054529	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs13058500	1.00[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1475978	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1475979	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs16991028	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs16991084	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs4821089	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754227	0.83[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs725337	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725338	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7286819	0.90[CHB][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs731933	0.95[CHB][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs743741	0.93[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs743742	0.81[ASW][hapmap];0.83[MEX][hapmap]
rs743744	0.95[CHB][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9621545	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064719	chr22:33028891-33159636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv588897	chr22:33116314-33139230	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12484015	RFPL1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33112200-33121400	Enhancers	Fetal Thymus	thymus
2	chr22:33113000-33121600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr22:33114400-33121400	Weak transcription	Colon Smooth Muscle	Colon
4	chr22:33114600-33121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr22:33115800-33122200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr22:33116800-33121600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:33116800-33121800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr22:33117400-33124200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:33118400-33121400	Enhancers	Primary hematopoietic stem cells	blood
10	chr22:33118600-33121800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr22:33118800-33121400	Enhancers	Adipose Nuclei	Adipose
12	chr22:33119000-33121800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr22:33119800-33121400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:33120000-33122000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:33120000-33124200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr22:33120000-33129600	Weak transcription	Right Atrium	heart
17	chr22:33120400-33121400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr22:33120400-33121400	Weak transcription	Osteobl	bone
19	chr22:33120600-33121800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr22:33120800-33127400	Weak transcription	Thymus	Thymus
21	chr22:33121000-33121800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr22:33121000-33124200	Weak transcription	Dnd41	blood
23	chr22:33121200-33121400	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr22:33121200-33122000	Enhancers	HepG2	liver

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