Variant report

Variant	rs6670660
Chromosome Location	chr1:78048698-78048699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78046709..78049145-chr1:78443356..78446176,2	MCF-7	breast:
2	chr1:78047184..78050090-chr1:78059485..78061127,2	K562	blood:
3	chr1:78043897..78047210-chr1:78047677..78049469,3	K562	blood:

Variant related genes	Relation type
ENSG00000137960	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1038983	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10873955	0.82[EUR][1000 genomes]
rs11162365	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11162366	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11162368	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162369	0.87[EUR][1000 genomes]
rs11162370	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11162372	0.89[EUR][1000 genomes]
rs11162380	0.92[EUR][1000 genomes]
rs11162383	0.83[EUR][1000 genomes]
rs11162386	0.84[EUR][1000 genomes]
rs11162387	0.83[EUR][1000 genomes]
rs11578805	0.93[EUR][1000 genomes]
rs12026939	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12142671	0.86[EUR][1000 genomes]
rs12717767	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12717768	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1389789	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1389790	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1565851	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1565852	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs166770	0.81[EUR][1000 genomes]
rs1962523	0.86[AMR][1000 genomes]
rs203229	0.80[ASN][1000 genomes]
rs2147318	0.81[EUR][1000 genomes]
rs278833	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs278834	0.83[ASN][1000 genomes]
rs278836	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278837	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278843	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278847	0.84[EUR][1000 genomes]
rs278848	0.83[ASN][1000 genomes]
rs278850	0.83[ASN][1000 genomes]
rs278854	0.85[EUR][1000 genomes]
rs278855	0.83[ASN][1000 genomes]
rs278856	0.82[ASN][1000 genomes]
rs278857	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278858	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278859	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278860	0.83[ASN][1000 genomes]
rs278863	0.83[ASN][1000 genomes]
rs278864	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3509	0.83[AMR][1000 genomes]
rs366467	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs370335	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs371076	0.89[EUR][1000 genomes]
rs4949661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949814	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949816	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4949817	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949818	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4949822	0.83[EUR][1000 genomes]
rs56688304	0.82[EUR][1000 genomes]
rs574973	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6603955	0.83[EUR][1000 genomes]
rs6603956	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6657290	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661656	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6672200	0.90[EUR][1000 genomes]
rs6674638	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6687596	0.82[EUR][1000 genomes]
rs6691317	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698151	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699205	0.82[ASN][1000 genomes]
rs6699311	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs728741	0.86[AMR][1000 genomes]
rs7521042	0.85[EUR][1000 genomes]
rs7543125	0.81[EUR][1000 genomes]
rs7545175	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7546365	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552291	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556227	0.84[EUR][1000 genomes]
rs7556523	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs872342	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs962388	0.81[AMR][1000 genomes]
rs9662527	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9988619	0.81[EUR][1000 genomes];0.94[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
rs6670660	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	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
2	chr1:78023200-78050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:78023800-78048800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:78024800-78071000	Weak transcription	Gastric	stomach
5	chr1:78025400-78050600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:78026000-78049400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:78026400-78048800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:78026800-78049200	Weak transcription	Colonic Mucosa	Colon
9	chr1:78027200-78049800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:78028600-78054600	Weak transcription	Esophagus	oesophagus
11	chr1:78029800-78050600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:78030000-78048800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:78030200-78048800	Strong transcription	Fetal Intestine Large	intestine
14	chr1:78030200-78049400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:78030400-78050400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:78032000-78049000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:78032000-78062800	Weak transcription	Fetal Heart	heart
18	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
19	chr1:78032800-78070600	Weak transcription	Small Intestine	intestine
20	chr1:78033000-78057000	Weak transcription	Spleen	Spleen
21	chr1:78033000-78057200	Weak transcription	Psoas Muscle	Psoas
22	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:78033400-78057600	Weak transcription	Right Ventricle	heart
24	chr1:78033400-78069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:78033600-78051400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:78033600-78070800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:78034000-78056200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:78034400-78049400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:78036400-78052800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:78036600-78050200	Strong transcription	NHDF-Ad	bronchial
31	chr1:78036800-78049600	Strong transcription	Dnd41	blood
32	chr1:78037000-78048800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:78037000-78048800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:78037000-78050600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:78037200-78049000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:78037800-78055400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:78038000-78048800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:78038400-78050200	Strong transcription	Osteobl	bone
39	chr1:78038600-78053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:78038600-78071000	Weak transcription	Pancreas	Pancrea
41	chr1:78039000-78070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:78039800-78049000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:78039800-78049600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:78040200-78049600	Strong transcription	Fetal Lung	lung
45	chr1:78040400-78048800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:78041800-78050800	Weak transcription	Brain Angular Gyrus	brain
47	chr1:78042000-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:78042000-78074600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:78042200-78073800	Weak transcription	Fetal Brain Female	brain
50	chr1:78042800-78051800	Weak transcription	Brain Germinal Matrix	brain

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