Variant report

Variant	rs56688304
Chromosome Location	chr1:78233499-78233500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78231667..78234324-chr1:78242486..78244868,2	K562	blood:
2	chr1:78225774..78228799-chr1:78231164..78234244,5	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1038983	0.86[EUR][1000 genomes]
rs10873953	0.90[ASN][1000 genomes]
rs10873954	0.80[ASN][1000 genomes]
rs10873955	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162366	0.81[EUR][1000 genomes]
rs11162378	0.89[ASN][1000 genomes]
rs11162380	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11162383	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11162384	0.85[ASN][1000 genomes]
rs11162386	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162387	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11578805	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1166586	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166589	0.87[ASN][1000 genomes]
rs12026939	0.86[EUR][1000 genomes]
rs12090729	0.85[ASN][1000 genomes]
rs12128041	0.81[EUR][1000 genomes]
rs12132838	0.99[ASN][1000 genomes]
rs12135104	0.87[ASN][1000 genomes]
rs12142441	0.99[ASN][1000 genomes]
rs12142671	0.80[EUR][1000 genomes]
rs1539739	0.85[ASN][1000 genomes]
rs2031342	0.99[ASN][1000 genomes]
rs203229	0.83[ASN][1000 genomes]
rs2147318	0.83[EUR][1000 genomes]
rs2274123	0.81[EUR][1000 genomes]
rs2296227	0.93[ASN][1000 genomes]
rs278833	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278836	0.86[EUR][1000 genomes]
rs278840	0.87[ASN][1000 genomes]
rs278841	0.86[ASN][1000 genomes]
rs278842	0.87[ASN][1000 genomes]
rs278843	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278845	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278847	0.82[EUR][1000 genomes]
rs278848	0.82[ASN][1000 genomes]
rs278852	0.81[EUR][1000 genomes]
rs278855	0.82[ASN][1000 genomes]
rs278856	0.81[ASN][1000 genomes]
rs278857	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278858	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278859	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278860	0.82[ASN][1000 genomes]
rs278862	0.82[EUR][1000 genomes]
rs278863	0.82[ASN][1000 genomes]
rs278864	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs366467	0.86[EUR][1000 genomes]
rs370335	0.86[EUR][1000 genomes]
rs3767037	0.92[ASN][1000 genomes]
rs3767038	0.99[ASN][1000 genomes]
rs4488068	0.99[ASN][1000 genomes]
rs4949661	0.82[EUR][1000 genomes]
rs4949814	0.81[EUR][1000 genomes]
rs4949822	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5025902	0.84[EUR][1000 genomes]
rs6603956	0.86[EUR][1000 genomes]
rs6603958	0.89[ASN][1000 genomes]
rs6603960	0.94[ASN][1000 genomes]
rs6657290	0.86[EUR][1000 genomes]
rs6670660	0.82[EUR][1000 genomes]
rs6672200	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674638	0.85[EUR][1000 genomes]
rs6687501	0.93[ASN][1000 genomes]
rs6687596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691317	0.82[EUR][1000 genomes]
rs6693100	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6698151	0.82[EUR][1000 genomes]
rs717333	0.99[ASN][1000 genomes]
rs7519946	0.99[ASN][1000 genomes]
rs7535781	0.99[ASN][1000 genomes]
rs7536206	0.85[ASN][1000 genomes]
rs7543037	0.85[ASN][1000 genomes]
rs7543125	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7545175	0.82[EUR][1000 genomes]
rs7556227	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8179272	0.82[ASN][1000 genomes]
rs9662527	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	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
11	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
rs56688304	USP33	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78233400-78238200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links