Variant report

Variant	rs1328254
Chromosome Location	chr5:49560859-49560860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10038023	0.86[ASN][1000 genomes]
rs10053631	0.85[AMR][1000 genomes]
rs10053639	0.84[AMR][1000 genomes]
rs10055539	0.86[EUR][1000 genomes]
rs10056605	0.86[ASN][1000 genomes]
rs10062032	0.82[ASN][1000 genomes]
rs10066635	0.87[EUR][1000 genomes]
rs10068272	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10074359	0.82[ASN][1000 genomes]
rs10076490	0.83[EUR][1000 genomes]
rs1010676	0.90[JPT][hapmap]
rs1039797	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10461390	0.82[ASN][1000 genomes]
rs10461391	0.85[ASN][1000 genomes]
rs10471362	0.85[EUR][1000 genomes]
rs10940129	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740458	0.80[AMR][1000 genomes]
rs11950949	0.80[AMR][1000 genomes]
rs11953045	0.80[AMR][1000 genomes]
rs12513730	0.86[ASN][1000 genomes]
rs12519021	0.89[ASN][1000 genomes]
rs12651909	0.85[EUR][1000 genomes]
rs12655271	0.80[AMR][1000 genomes]
rs12697055	0.82[ASN][1000 genomes]
rs13157992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13173678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13182357	0.90[JPT][hapmap]
rs13185587	0.88[EUR][1000 genomes]
rs1511735	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1511737	0.85[ASN][1000 genomes]
rs1511738	0.82[ASN][1000 genomes]
rs1606224	0.83[ASN][1000 genomes]
rs1812936	0.90[JPT][hapmap]
rs1812994	0.88[EUR][1000 genomes]
rs1995795	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2036901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2036902	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2089605	0.83[EUR][1000 genomes]
rs2137129	0.86[ASN][1000 genomes]
rs2137132	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2199090	0.86[ASN][1000 genomes]
rs2199092	0.88[ASN][1000 genomes]
rs2271236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2352789	0.92[ASN][1000 genomes]
rs2353222	0.85[AMR][1000 genomes]
rs2668024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs28445612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2883164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs303219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs303235	0.86[EUR][1000 genomes]
rs303237	0.85[EUR][1000 genomes]
rs3849670	0.88[EUR][1000 genomes]
rs3950451	0.86[EUR][1000 genomes]
rs4030569	0.87[EUR][1000 genomes]
rs4030570	0.85[EUR][1000 genomes]
rs4030572	0.86[EUR][1000 genomes]
rs4030573	0.84[EUR][1000 genomes]
rs4249603	0.85[AMR][1000 genomes]
rs4321782	0.91[ASN][1000 genomes]
rs4446513	0.84[AMR][1000 genomes]
rs4549528	0.86[EUR][1000 genomes]
rs4571473	0.86[EUR][1000 genomes]
rs471455	0.87[ASN][1000 genomes]
rs472278	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs481222	0.97[ASN][1000 genomes]
rs485101	0.80[ASN][1000 genomes]
rs4865519	0.83[ASN][1000 genomes]
rs4865522	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4865550	0.82[AMR][1000 genomes]
rs4865552	0.85[AMR][1000 genomes]
rs4865698	0.83[ASN][1000 genomes]
rs4865699	0.83[ASN][1000 genomes]
rs4865700	0.83[ASN][1000 genomes]
rs4865727	0.81[AMR][1000 genomes]
rs494540	0.87[ASN][1000 genomes]
rs496108	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs498951	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5011669	0.82[ASN][1000 genomes]
rs504520	0.83[ASN][1000 genomes]
rs507396	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511188	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs527170	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs531198	0.81[ASN][1000 genomes]
rs534123	0.85[ASN][1000 genomes]
rs535100	0.84[ASN][1000 genomes]
rs535113	0.87[ASN][1000 genomes]
rs547563	0.82[ASN][1000 genomes]
rs552892	0.95[ASN][1000 genomes]
rs559096	0.88[ASN][1000 genomes]
rs560861	0.81[ASN][1000 genomes]
rs577482	0.82[AMR][1000 genomes]
rs6449961	0.81[ASN][1000 genomes]
rs6869871	0.83[EUR][1000 genomes]
rs6874829	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6876902	0.84[ASN][1000 genomes]
rs72768421	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7293426	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7341010	0.82[ASN][1000 genomes]
rs7442966	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7446360	0.83[EUR][1000 genomes]
rs7446951	0.82[ASN][1000 genomes]
rs7447926	0.82[ASN][1000 genomes]
rs7712749	0.81[EUR][1000 genomes]
rs7712849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7721808	0.88[EUR][1000 genomes]
rs7722742	0.81[ASN][1000 genomes]
rs8188088	0.83[AMR][1000 genomes]
rs8188203	0.85[AMR][1000 genomes]
rs9291925	0.81[ASN][1000 genomes]
rs9292005	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv15107	chr5:49405763-49562327	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv2760950	chr5:49432831-49624358	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1025722	chr5:49455624-49561216	ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1016253	chr5:49455624-49564818	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1034447	chr5:49455624-49568948	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1015794	chr5:49455624-49572706	ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1021120	chr5:49455624-49583553	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1034906	chr5:49455624-49586503	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1016533	chr5:49455624-49587789	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1033970	chr5:49455624-49595874	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1032046	chr5:49455624-49597527	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1021477	chr5:49455624-49624358	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv1020912	chr5:49542837-49624358	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1328254	EMB	cis	parietal	SCAN
rs1328254	EMB	cis	Thyroid	GTEx
rs1328254	LOC647121	trans	multi-tissue	Pritchard
rs1328254	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs1328254	ARL15	cis	parietal	SCAN
rs1328254	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49560800-49561000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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