Variant report

Variant	rs4656352
Chromosome Location	chr1:162065422-162065423
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:162053008..162055222-chr1:162063836..162065788,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10157090	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10159401	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10494366	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10737536	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753754	0.85[EUR][1000 genomes]
rs10753762	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10800298	0.83[EUR][1000 genomes]
rs10800301	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10800303	0.85[EUR][1000 genomes]
rs10800305	0.85[EUR][1000 genomes]
rs10800307	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800311	0.84[EUR][1000 genomes]
rs10918630	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10918671	0.85[EUR][1000 genomes]
rs10918680	0.84[EUR][1000 genomes]
rs10918681	0.83[EUR][1000 genomes]
rs10918684	0.85[EUR][1000 genomes]
rs10918687	0.84[EUR][1000 genomes]
rs10918688	0.84[EUR][1000 genomes]
rs11579080	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11579850	0.85[EUR][1000 genomes]
rs11580365	0.85[EUR][1000 genomes]
rs11808624	0.83[EUR][1000 genomes]
rs12033159	0.92[ASN][1000 genomes]
rs12036268	0.92[ASN][1000 genomes]
rs12036529	0.92[ASN][1000 genomes]
rs12406484	0.85[EUR][1000 genomes]
rs12406785	0.85[EUR][1000 genomes]
rs12407513	0.84[EUR][1000 genomes]
rs12727141	0.84[EUR][1000 genomes]
rs12727810	0.85[EUR][1000 genomes]
rs12733821	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1337060	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337061	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337062	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415256	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415257	0.85[EUR][1000 genomes]
rs1415258	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415259	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415260	0.84[EUR][1000 genomes]
rs1415264	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1415265	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1572498	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1572499	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1577771	0.92[ASN][1000 genomes]
rs2095626	0.85[EUR][1000 genomes]
rs2210942	0.85[EUR][1000 genomes]
rs2225845	0.81[AMR][1000 genomes]
rs2225846	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2225847	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922867	0.84[EUR][1000 genomes]
rs4098274	0.85[AMR][1000 genomes]
rs4656348	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4656349	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4656350	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657140	0.84[EUR][1000 genomes]
rs4657141	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4657142	0.85[EUR][1000 genomes]
rs4657143	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657145	0.84[EUR][1000 genomes]
rs4657152	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657154	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657155	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5000342	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6413902	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427650	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6427651	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6664115	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672881	0.84[EUR][1000 genomes]
rs6684179	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6684278	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6688966	0.85[EUR][1000 genomes]
rs6696160	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7417931	0.85[EUR][1000 genomes]
rs7512106	0.92[ASN][1000 genomes]
rs7521236	0.85[EUR][1000 genomes]
rs7534045	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7538490	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541332	0.85[EUR][1000 genomes]
rs7551959	0.84[EUR][1000 genomes]
rs945706	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1821140	chr1:162047541-162389040	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv1818566	chr1:162061209-162430009	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	esv1823751	chr1:162063023-162344102	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv1821064	chr1:162063023-162363991	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	esv2756867	chr1:162064468-162360008	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	esv1822491	chr1:162064468-162369410	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	esv2758973	chr1:162064468-162503356	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv1822160	chr1:162064487-162386000	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	esv1824093	chr1:162064506-162363104	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	esv1823861	chr1:162064544-162363263	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
16	esv1819558	chr1:162064587-162091284	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	esv1824795	chr1:162065253-162363732	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:162062200-162065800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:162062200-162069000	Weak transcription	Pancreas	Pancrea
3	chr1:162063000-162068000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:162063000-162068000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:162063200-162067400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:162063200-162074400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:162063200-162077400	Weak transcription	Liver	Liver
8	chr1:162064800-162077200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links