Variant report

Variant	rs4488068
Chromosome Location	chr1:78242837-78242838
allele	A/G
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	chr1:78242233-78243442	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:78236523..78239438-chr1:78241611..78243402,2	K562	blood:
2	chr1:78223366..78226261-chr1:78240753..78243357,2	K562	blood:
3	chr1:78231667..78234324-chr1:78242486..78244868,2	K562	blood:
4	chr1:78239127..78242956-chr1:78244047..78246428,3	K562	blood:

Variant related genes	Relation type
FAM73A	TF binding region
RNA5SP21	TF binding region
ENSG00000232672	TF binding region
ENSG00000077254	Chromatin interaction
ENSG00000222849	Chromatin interaction
ENSG00000180488	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10873953	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10873954	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10873955	0.86[ASN][1000 genomes]
rs11162368	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162370	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162374	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11162378	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11162380	0.91[ASN][1000 genomes]
rs11162383	0.85[ASN][1000 genomes]
rs11162384	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11162386	0.86[ASN][1000 genomes]
rs11162387	0.86[ASN][1000 genomes]
rs11578805	0.89[ASN][1000 genomes]
rs1166586	0.87[ASN][1000 genomes]
rs1166589	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12090729	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12132838	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12135104	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12717768	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1389789	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1389790	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1539739	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs166770	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2031342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203229	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296227	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278832	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278833	0.82[ASN][1000 genomes]
rs278834	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278837	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278840	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278841	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278842	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278843	0.82[ASN][1000 genomes]
rs278844	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278848	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs278850	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278851	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278855	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs278856	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs278857	0.80[ASN][1000 genomes]
rs278858	0.80[ASN][1000 genomes]
rs278859	0.80[ASN][1000 genomes]
rs278860	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs278863	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs278864	0.80[ASN][1000 genomes]
rs3767037	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767038	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949817	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4949818	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949822	0.86[ASN][1000 genomes]
rs56688304	0.99[ASN][1000 genomes]
rs574973	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6603958	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6603960	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661656	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6672200	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687501	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6687596	0.99[ASN][1000 genomes]
rs6699205	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6699311	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs717333	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519946	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535781	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7536206	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7543037	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7543125	0.86[ASN][1000 genomes]
rs7546365	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7556227	0.86[ASN][1000 genomes]
rs7556523	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8179272	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs872342	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9662527	0.87[ASN][1000 genomes]
rs9988619	0.83[AMR][1000 genomes];0.87[EUR][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	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
9	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
10	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
11	nsv946005	chr1:78237708-78244726	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4488068	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78239600-78245000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:78240000-78245000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:78240200-78245200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:78240200-78245200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:78240400-78245200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:78242400-78243000	Enhancers	Placenta	Placenta
7	chr1:78242800-78244800	Weak transcription	HepG2	liver

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