Variant report

Variant	rs725338
Chromosome Location	chr22:33120576-33120577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11089591	0.84[ASN][1000 genomes]
rs12484015	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]
rs12484429	0.81[ASN][1000 genomes]
rs13054529	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs13058500	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs1475978	0.82[CHD][hapmap]
rs1475979	0.84[CHD][hapmap]
rs16991028	0.82[CHD][hapmap]
rs16991084	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs2899193	0.82[CHB][hapmap]
rs4821089	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]
rs5754227	0.82[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs725337	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7286819	0.84[ASN][1000 genomes]
rs731933	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs743741	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs743744	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs8136470	0.81[ASN][1000 genomes]
rs9621545	0.84[JPT][hapmap];0.84[MEX][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs725338	RFPL1	cis	cerebellum	SCAN
rs725338	RNF185	cis	parietal	SCAN
rs725338	GAS2L1	cis	parietal	SCAN

Chromatin state (count:41 , 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	chr22:33116400-33120600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr22:33116600-33120800	Enhancers	Fetal Stomach	stomach
8	chr22:33116800-33121600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr22:33116800-33121800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr22:33117200-33120600	Enhancers	HMEC	breast
11	chr22:33117400-33121000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:33117400-33124200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:33118400-33120600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr22:33118400-33121200	Weak transcription	HepG2	liver
15	chr22:33118400-33121400	Enhancers	Primary hematopoietic stem cells	blood
16	chr22:33118600-33120600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr22:33118600-33120600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr22:33118600-33121800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr22:33118800-33120600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:33118800-33121400	Enhancers	Adipose Nuclei	Adipose
21	chr22:33119000-33120600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr22:33119000-33120600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr22:33119000-33120600	Enhancers	Fetal Lung	lung
24	chr22:33119000-33120800	Enhancers	Duodenum Mucosa	Duodenum
25	chr22:33119000-33121200	Enhancers	Placenta	Placenta
26	chr22:33119000-33121800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr22:33119800-33121400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr22:33120000-33120600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr22:33120000-33120600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr22:33120000-33120600	Enhancers	NHEK	skin
31	chr22:33120000-33120800	Enhancers	Primary T cells from cord blood	blood
32	chr22:33120000-33120800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr22:33120000-33120800	Enhancers	Thymus	Thymus
34	chr22:33120000-33122000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr22:33120000-33124200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr22:33120000-33129600	Weak transcription	Right Atrium	heart
37	chr22:33120200-33120800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr22:33120200-33121000	Enhancers	Dnd41	blood
39	chr22:33120200-33121200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr22:33120400-33121400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr22:33120400-33121400	Weak transcription	Osteobl	bone

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