Variant report

Variant	rs6603960
Chromosome Location	chr1:78213434-78213435
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:78212782-78213568	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78194894..78198159-chr1:78213039..78215379,3	K562	blood:
2	chr1:78212750..78216522-chr1:78224934..78227358,4	MCF-7	breast:

Variant related genes	Relation type
USP33	TF binding region
ENSG00000077254	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1038983	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10873951	0.85[CEU][hapmap]
rs10873953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10873954	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10873955	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11162368	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11162370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11162374	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162378	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11162384	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162386	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11162387	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs11578805	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1166586	0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1166589	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12090729	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12132838	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12135104	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12142441	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12717768	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1389789	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1389790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1539739	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs166770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2031342	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs203229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088058	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2296227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278832	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278833	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278834	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278836	0.81[ASN][1000 genomes]
rs278837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278840	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278841	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278843	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278844	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278851	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs278855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278856	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278857	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278858	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278859	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278860	0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278864	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs370335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3767037	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767038	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4488068	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949814	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4949817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4949818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56688304	0.94[ASN][1000 genomes]
rs574973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6603956	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6603958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657290	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6661656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6672200	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6687596	0.94[ASN][1000 genomes]
rs6699205	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6699311	1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs717333	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519946	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535781	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536206	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7543037	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7546365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7552291	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7556523	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8179272	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs872342	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9662527	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9988619	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1798160	chr1:78149941-78267421	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	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
8	nsv508326	chr1:78184379-78234247	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6603960	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78173800-78224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:78191600-78215600	Weak transcription	A549	lung
3	chr1:78192000-78215000	Weak transcription	HSMMtube	muscle
4	chr1:78192200-78222400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:78193000-78221200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:78193600-78222600	Weak transcription	Fetal Kidney	kidney
7	chr1:78194400-78214400	Weak transcription	NHLF	lung
8	chr1:78194400-78223400	Weak transcription	NH-A	brain
9	chr1:78194600-78215200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:78195200-78214000	Weak transcription	Small Intestine	intestine
11	chr1:78195400-78216000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:78195400-78216800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:78195400-78222200	Weak transcription	Gastric	stomach
14	chr1:78195400-78223200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:78195400-78224200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:78195400-78224800	Weak transcription	Spleen	Spleen
17	chr1:78196800-78221800	Weak transcription	Ovary	ovary
18	chr1:78197800-78215000	Weak transcription	Fetal Stomach	stomach
19	chr1:78197800-78221800	Weak transcription	Thymus	Thymus
20	chr1:78197800-78222400	Weak transcription	Fetal Intestine Small	intestine
21	chr1:78197800-78223400	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:78198200-78222200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:78198400-78224000	Weak transcription	Esophagus	oesophagus
24	chr1:78200200-78218800	Weak transcription	HUVEC	blood vessel
25	chr1:78202800-78217000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:78205200-78214600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:78205400-78220200	Weak transcription	GM12878-XiMat	blood
28	chr1:78205400-78221800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:78205600-78222200	Weak transcription	Fetal Brain Male	brain
30	chr1:78205800-78213600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:78206000-78214800	Weak transcription	Brain Anterior Caudate	brain
32	chr1:78206000-78216000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:78206000-78216800	Weak transcription	Primary T cells from cord blood	blood
34	chr1:78206000-78222000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:78206000-78222200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:78206000-78224400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:78206200-78214600	Weak transcription	Osteobl	bone
38	chr1:78206400-78222000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:78206400-78222400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:78206400-78224000	Weak transcription	Fetal Intestine Large	intestine
41	chr1:78206400-78224000	Weak transcription	HSMM	muscle
42	chr1:78206600-78213600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:78206600-78215800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:78206600-78220200	Weak transcription	Dnd41	blood
45	chr1:78206600-78220800	Weak transcription	Hela-S3	cervix
46	chr1:78206600-78221000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:78206600-78221200	Weak transcription	Fetal Thymus	thymus
48	chr1:78206600-78221400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:78206600-78221600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:78206600-78222000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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