Variant report

Variant	rs2147318
Chromosome Location	chr1:78242638-78242639
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
RNA5SP21	TF binding region
FAM73A	TF binding region
ENSG00000232672	TF binding region
ENSG00000180488	Chromatin interaction
ENSG00000077254	Chromatin interaction
ENSG00000222849	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1038983	0.94[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10873951	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs10873955	0.94[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11162365	0.87[EUR][1000 genomes]
rs11162369	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11162372	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162380	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11162383	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11162386	0.94[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11162387	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11578805	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1166584	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1166585	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1166586	0.82[CEU][hapmap]
rs1166588	0.88[ASW][hapmap];0.83[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12026939	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12128041	0.88[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12142441	0.81[GIH][hapmap]
rs12142671	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12717767	0.87[EUR][1000 genomes]
rs1565852	0.89[EUR][1000 genomes]
rs1977900	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2031342	0.81[GIH][hapmap]
rs2274123	0.83[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278833	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278836	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs278843	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278845	0.84[EUR][1000 genomes]
rs278847	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs278852	0.82[EUR][1000 genomes]
rs278854	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs278857	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278858	0.94[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278859	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs278862	0.83[EUR][1000 genomes]
rs278864	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs366467	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs370335	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs371076	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3767038	0.81[GIH][hapmap]
rs4949661	0.81[EUR][1000 genomes]
rs4949816	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4949822	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5025902	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56688304	0.83[EUR][1000 genomes]
rs6603955	0.80[EUR][1000 genomes]
rs6603956	0.94[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6657290	0.94[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6670660	0.81[EUR][1000 genomes]
rs6672200	0.94[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6674638	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6687596	0.83[EUR][1000 genomes]
rs6691317	0.80[EUR][1000 genomes]
rs6693100	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6698151	0.81[EUR][1000 genomes]
rs717333	0.81[GIH][hapmap]
rs7513619	0.83[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7521042	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7535781	0.81[GIH][hapmap]
rs7543125	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7545175	0.81[EUR][1000 genomes]
rs7556227	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs872342	0.89[JPT][hapmap]
rs9662527	0.94[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2147318	AK5	cis	parietal	SCAN
rs2147318	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	chr1:78241800-78242800	Enhancers	HepG2	liver
7	chr1:78242400-78243000	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links