Variant report

Variant	rs4821089
Chromosome Location	chr22:33118165-33118166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10854628	0.83[CHB][hapmap]
rs11089591	0.90[ASN][1000 genomes]
rs12484015	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]
rs12484429	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs13054529	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][1000 genomes]
rs13058500	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1475978	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs1475979	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs16991028	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs16991084	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[ASN][1000 genomes]
rs2899193	0.82[AMR][1000 genomes]
rs3827339	0.83[CHB][hapmap];0.83[YRI][hapmap]
rs5754227	0.87[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs725337	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725338	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7286819	0.95[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7289865	0.81[ASN][1000 genomes]
rs7291198	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs731933	1.00[CHB][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs743741	0.93[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs743742	0.81[ASW][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs743744	1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs743745	0.83[CHB][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs9619301	0.83[CHB][hapmap]
rs9621545	0.84[JPT][hapmap]
rs997120	0.83[CHB][hapmap];0.83[CHD][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
rs4821089	RFPL1	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33111000-33118600	Weak transcription	HSMMtube	muscle
2	chr22:33112200-33121400	Enhancers	Fetal Thymus	thymus
3	chr22:33113000-33121600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr22:33113400-33120400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr22:33114200-33119400	Weak transcription	Esophagus	oesophagus
6	chr22:33114400-33119000	Weak transcription	Small Intestine	intestine
7	chr22:33114400-33119400	Weak transcription	Left Ventricle	heart
8	chr22:33114400-33121400	Weak transcription	Colon Smooth Muscle	Colon
9	chr22:33114600-33121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:33115600-33119600	Enhancers	Thymus	Thymus
11	chr22:33115800-33119400	Enhancers	Dnd41	blood
12	chr22:33115800-33122200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr22:33116000-33119400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:33116000-33119600	Enhancers	Primary T cells from cord blood	blood
15	chr22:33116200-33119400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr22:33116400-33119600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr22:33116400-33120400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr22:33116400-33120600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr22:33116600-33120400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr22:33116600-33120400	Enhancers	Osteobl	bone
21	chr22:33116600-33120800	Enhancers	Fetal Stomach	stomach
22	chr22:33116800-33118200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr22:33116800-33118200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr22:33116800-33120400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:33116800-33121600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr22:33116800-33121800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr22:33117000-33119200	Weak transcription	Fetal Kidney	kidney
28	chr22:33117000-33119400	Weak transcription	Colonic Mucosa	Colon
29	chr22:33117200-33118400	Enhancers	HepG2	liver
30	chr22:33117200-33118600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr22:33117200-33119000	Weak transcription	NH-A	brain
32	chr22:33117200-33120600	Enhancers	HMEC	breast
33	chr22:33117400-33118200	Weak transcription	Spleen	Spleen
34	chr22:33117400-33118400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr22:33117400-33118400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr22:33117400-33118400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr22:33117400-33118400	Weak transcription	Fetal Muscle Leg	muscle
38	chr22:33117400-33118600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr22:33117400-33118600	Weak transcription	Right Atrium	heart
40	chr22:33117400-33118800	Weak transcription	Adipose Nuclei	Adipose
41	chr22:33117400-33118800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr22:33117400-33118800	Weak transcription	NHEK	skin
43	chr22:33117400-33119000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr22:33117400-33119000	Weak transcription	Fetal Lung	lung
45	chr22:33117400-33119000	Weak transcription	NHDF-Ad	bronchial
46	chr22:33117400-33119200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr22:33117400-33119400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr22:33117400-33119600	Weak transcription	Fetal Intestine Large	intestine
49	chr22:33117400-33121000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr22:33117400-33124200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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