Variant report

Variant	rs1546817
Chromosome Location	chr3:60459187-60459188
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11924296	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947161	0.86[CHD][hapmap]
rs1996828	0.95[CEU][hapmap]
rs1996829	0.95[CEU][hapmap]
rs2121861	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2121862	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2121863	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs2166824	0.86[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2594248	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2594250	0.95[CEU][hapmap]
rs2687193	0.95[CEU][hapmap]
rs2687194	0.95[CEU][hapmap]
rs2734390	0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs3856654	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.88[ASN][1000 genomes]
rs3901943	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234288	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439087	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4393860	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440692	0.86[CHD][hapmap]
rs4468936	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452392	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs453951	0.83[CHB][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs4638920	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs4679478	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473944	0.86[CHD][hapmap]
rs7644852	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7644970	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645058	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs885737	0.81[EUR][1000 genomes]
rs9820943	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826530	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9830999	0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9846621	0.81[EUR][1000 genomes]
rs9852001	0.86[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9856092	0.81[CEU][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9868373	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv997531	chr3:60340440-60504992	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1010314	chr3:60367530-60459926	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1008235	chr3:60388277-60558331	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv460569	chr3:60388322-60558331	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv590399	chr3:60388322-60558331	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2763271	chr3:60391557-60558331	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv999284	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1002453	chr3:60391557-60558331	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv948513	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1008661	chr3:60397271-60558331	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1005085	chr3:60397612-60532440	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv460570	chr3:60418362-60465139	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv590401	chr3:60418362-60465139	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv876853	chr3:60420665-60512889	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1010907	chr3:60425237-60557503	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1002978	chr3:60425237-60558331	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv876854	chr3:60432292-60472209	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1001005	chr3:60433224-60472410	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv524767	chr3:60438026-60531242	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv590402	chr3:60438026-60536420	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv2762330	chr3:60441341-60466842	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	diseases
25	nsv532625	chr3:60445746-60517859	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv876855	chr3:60448261-60500549	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv1014064	chr3:60448591-60558331	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60458600-60459200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr3:60458800-60459200	Enhancers	Brain Germinal Matrix	brain
3	chr3:60458800-60459400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:60458800-60459400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links