Variant report

Variant	rs4949822
Chromosome Location	chr1:78272902-78272903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1038983	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10873954	0.96[ASN][1000 genomes]
rs10873955	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162366	0.81[EUR][1000 genomes]
rs11162369	0.80[AMR][1000 genomes]
rs11162372	0.80[AMR][1000 genomes]
rs11162380	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162383	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162384	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162386	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162387	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578805	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1166584	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1166586	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1166589	0.97[ASN][1000 genomes]
rs12026939	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12090729	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132838	0.84[ASN][1000 genomes]
rs12142441	0.86[ASN][1000 genomes]
rs12142671	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1539739	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977900	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2031342	0.86[ASN][1000 genomes]
rs2147318	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278833	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278836	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278843	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278847	0.84[AMR][1000 genomes]
rs278854	0.80[AMR][1000 genomes]
rs278857	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278858	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278859	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278864	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs366467	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs370335	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs371076	0.80[AMR][1000 genomes]
rs3767038	0.84[ASN][1000 genomes]
rs4488068	0.86[ASN][1000 genomes]
rs4949661	0.83[EUR][1000 genomes]
rs4949814	0.81[EUR][1000 genomes]
rs56688304	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6603956	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6657290	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6670660	0.83[EUR][1000 genomes]
rs6672200	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6674638	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6687596	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6691317	0.83[EUR][1000 genomes]
rs6698151	0.83[EUR][1000 genomes]
rs717333	0.84[ASN][1000 genomes]
rs7519946	0.84[ASN][1000 genomes]
rs7521042	0.82[AMR][1000 genomes]
rs7535781	0.84[ASN][1000 genomes]
rs7536206	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543037	1.00[ASN][1000 genomes]
rs7543125	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545175	0.83[EUR][1000 genomes]
rs7552291	0.80[EUR][1000 genomes]
rs7556227	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179272	0.97[ASN][1000 genomes]
rs9662527	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4949822	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78246000-78284200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:78246000-78285600	Weak transcription	Colonic Mucosa	Colon
3	chr1:78246200-78279400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:78246200-78279600	Weak transcription	Aorta	Aorta
5	chr1:78246400-78273200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:78246400-78274000	Weak transcription	Fetal Kidney	kidney
7	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
8	chr1:78246600-78274200	Weak transcription	HMEC	breast
9	chr1:78247400-78278400	Weak transcription	Hela-S3	cervix
10	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
11	chr1:78250400-78282400	Weak transcription	NHEK	skin
12	chr1:78250600-78279000	Weak transcription	NHLF	lung
13	chr1:78252200-78282600	Weak transcription	Right Ventricle	heart
14	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
15	chr1:78253000-78273200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:78253000-78279400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:78253000-78283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:78254400-78274000	Weak transcription	HSMMtube	muscle
19	chr1:78254400-78287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:78260000-78275400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:78260600-78279800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:78261000-78273400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:78261600-78275200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:78262800-78273200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:78262800-78285200	Weak transcription	Gastric	stomach
26	chr1:78263400-78275200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:78264600-78273800	Weak transcription	Brain Anterior Caudate	brain
28	chr1:78264600-78274400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:78266000-78298000	Weak transcription	K562	blood
30	chr1:78266200-78275400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:78266200-78299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:78266200-78299200	Weak transcription	Pancreas	Pancrea
33	chr1:78266400-78279400	Weak transcription	Brain Angular Gyrus	brain
34	chr1:78266600-78273000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:78266600-78284200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:78267200-78275200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:78267200-78279400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:78267600-78275400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:78267800-78275000	Strong transcription	Fetal Lung	lung
40	chr1:78267800-78275200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:78267800-78275200	Strong transcription	Fetal Intestine Large	intestine
42	chr1:78267800-78275400	Strong transcription	Placenta	Placenta
43	chr1:78268200-78275000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr1:78268400-78273200	Weak transcription	GM12878-XiMat	blood
45	chr1:78268400-78291200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:78268600-78274400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:78269200-78274600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:78269400-78275200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:78269800-78273600	Strong transcription	Brain Germinal Matrix	brain
50	chr1:78270200-78274200	Weak transcription	Fetal Brain Male	brain

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