Variant report

Variant	rs5763923
Chromosome Location	chr22:30675217-30675218
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10376	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10427610	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1043099	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2108093	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299830	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4339043	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4820008	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4820831	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4820844	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4823085	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5749066	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5749078	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5749082	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs5753071	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5753080	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5753088	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs5753111	0.90[ASN][1000 genomes]
rs737950	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs740219	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs757869	0.85[CHB][hapmap]
rs929454	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9608904	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9619104	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv588885	chr22:30661184-30691631	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5763923	SF3A1	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30669400-30676800	Enhancers	Adipose Nuclei	Adipose
2	chr22:30671600-30675600	Enhancers	Fetal Intestine Small	intestine
3	chr22:30672200-30676400	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr22:30672600-30675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr22:30672600-30678400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr22:30672600-30684400	Weak transcription	Fetal Brain Female	brain
7	chr22:30672800-30675400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr22:30672800-30678200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr22:30673000-30675600	Enhancers	Osteobl	bone
10	chr22:30673000-30675800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr22:30673000-30676000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr22:30673000-30676000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr22:30673000-30676000	Enhancers	HMEC	breast
14	chr22:30673000-30676200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr22:30673200-30675600	Enhancers	Fetal Intestine Large	intestine
16	chr22:30673200-30676000	Enhancers	Liver	Liver
17	chr22:30673200-30676400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr22:30673200-30676400	Enhancers	Dnd41	blood
19	chr22:30673200-30678200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr22:30673400-30676800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr22:30673400-30677000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr22:30673600-30675800	Enhancers	Fetal Muscle Trunk	muscle
23	chr22:30673600-30676000	Enhancers	Brain Substantia Nigra	brain
24	chr22:30673600-30676200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr22:30673600-30676200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr22:30673600-30676400	Enhancers	Placenta	Placenta
27	chr22:30673800-30675400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr22:30673800-30675400	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr22:30673800-30676000	Enhancers	Brain Hippocampus Middle	brain
30	chr22:30673800-30676000	Enhancers	Spleen	Spleen
31	chr22:30673800-30676000	Enhancers	NHDF-Ad	bronchial
32	chr22:30674000-30675400	Enhancers	Brain Angular Gyrus	brain
33	chr22:30674000-30676000	Enhancers	Esophagus	oesophagus
34	chr22:30674000-30676000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr22:30674000-30676000	Enhancers	NHLF	lung
36	chr22:30674000-30678800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr22:30674000-30680400	Weak transcription	A549	lung
38	chr22:30674200-30675800	Weak transcription	Stomach Mucosa	stomach
39	chr22:30674200-30676000	Enhancers	HUVEC	blood vessel
40	chr22:30674200-30676200	Enhancers	Lung	lung
41	chr22:30674200-30679200	Weak transcription	K562	blood
42	chr22:30674200-30679400	Weak transcription	Ovary	ovary
43	chr22:30674400-30675400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr22:30674400-30675400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr22:30674400-30676000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr22:30674400-30676400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr22:30674400-30678000	Weak transcription	Fetal Stomach	stomach
48	chr22:30674400-30678400	Weak transcription	Fetal Thymus	thymus
49	chr22:30674400-30680200	Weak transcription	Right Ventricle	heart
50	chr22:30674400-30680800	Weak transcription	Fetal Lung	lung

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