Variant report

Variant	rs9988619
Chromosome Location	chr1:78057291-78057292
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78053952..78055571-chr1:78057037..78059846,2	MCF-7	breast:
2	chr1:78053424..78055384-chr1:78055842..78057963,2	K562	blood:
3	chr1:78056022..78058450-chr1:78065873..78067883,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1038983	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873951	0.85[EUR][1000 genomes]
rs10873953	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11162366	0.94[ASN][1000 genomes]
rs11162368	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162370	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162374	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162378	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11162384	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11578805	0.80[ASN][1000 genomes]
rs1166589	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12026939	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12090729	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12132838	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12135104	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12142441	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12717768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389789	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1389790	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1539739	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs166770	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2031342	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs203229	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2088058	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2296227	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs278832	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs278833	0.82[ASN][1000 genomes]
rs278834	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278836	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278837	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278840	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278841	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278842	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278843	0.87[ASN][1000 genomes]
rs278844	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278848	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278850	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278851	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278855	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278856	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278857	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278858	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278859	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278860	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278863	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278864	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs366467	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs370335	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3767037	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3767038	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4488068	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4949661	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4949814	0.96[ASN][1000 genomes]
rs4949817	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949818	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs574973	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6603956	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6603958	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6603960	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6657290	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661656	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6670660	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674638	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6687501	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6691317	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698151	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699205	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6699311	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs717333	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7519946	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7535781	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7536206	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7543037	0.83[EUR][1000 genomes]
rs7545175	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552291	0.96[ASN][1000 genomes]
rs7556523	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8179272	0.84[AMR][1000 genomes]
rs872342	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9662527	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9988619	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
2	chr1:78024800-78071000	Weak transcription	Gastric	stomach
3	chr1:78032000-78062800	Weak transcription	Fetal Heart	heart
4	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
5	chr1:78032800-78070600	Weak transcription	Small Intestine	intestine
6	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:78033400-78057600	Weak transcription	Right Ventricle	heart
8	chr1:78033400-78069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:78033600-78070800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:78038600-78071000	Weak transcription	Pancreas	Pancrea
11	chr1:78039000-78070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:78042000-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:78042000-78074600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:78042200-78073800	Weak transcription	Fetal Brain Female	brain
15	chr1:78043000-78070200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:78044200-78069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:78044400-78063000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:78047000-78070800	Weak transcription	Lung	lung
19	chr1:78047000-78071200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:78047600-78060200	Weak transcription	HUVEC	blood vessel
21	chr1:78047600-78061800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:78047600-78062200	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:78047600-78063000	Weak transcription	Fetal Brain Male	brain
24	chr1:78047600-78063200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:78047600-78069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:78047600-78070800	Weak transcription	HSMMtube	muscle
27	chr1:78047600-78071000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:78047600-78071600	Weak transcription	Thymus	Thymus
29	chr1:78047600-78072400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:78047600-78072600	Weak transcription	Fetal Kidney	kidney
31	chr1:78047600-78074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:78047600-78074800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:78047600-78085600	Weak transcription	NHLF	lung
34	chr1:78047800-78058600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:78047800-78061800	Weak transcription	HSMM	muscle
36	chr1:78047800-78063000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:78047800-78063200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:78047800-78063200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:78047800-78070800	Weak transcription	Left Ventricle	heart
40	chr1:78047800-78070800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:78047800-78071000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:78047800-78074200	Weak transcription	Hela-S3	cervix
43	chr1:78047800-78074800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:78047800-78086200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:78047800-78090000	Weak transcription	NH-A	brain
46	chr1:78048000-78062600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:78048000-78074600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:78048000-78077800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:78048000-78097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:78048200-78062400	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links