Variant report

Variant	rs559096
Chromosome Location	chr5:49522346-49522347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49521747..49523250-chr8:46849640..46851140,2	MCF-7	breast:

Extended variants
information (count: 177 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10038023	0.83[EUR][1000 genomes]
rs10054827	0.83[AMR][1000 genomes]
rs10057362	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10062087	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10067381	0.86[AMR][1000 genomes]
rs1010676	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs10461391	0.80[EUR][1000 genomes]
rs10471784	0.91[AMR][1000 genomes]
rs10940090	0.90[AMR][1000 genomes]
rs10940514	0.91[AMR][1000 genomes]
rs10940520	0.91[AMR][1000 genomes]
rs10940533	0.91[AMR][1000 genomes]
rs10940646	0.90[AMR][1000 genomes]
rs11514621	0.94[AMR][1000 genomes]
rs11742067	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11748483	0.83[AMR][1000 genomes]
rs11749165	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950947	0.85[AMR][1000 genomes]
rs11953016	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12513730	0.81[EUR][1000 genomes]
rs12515555	0.80[AMR][1000 genomes]
rs12517502	0.89[AMR][1000 genomes]
rs12519021	0.83[ASN][1000 genomes]
rs12521333	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12521903	0.91[AMR][1000 genomes]
rs12655271	0.89[ASN][1000 genomes]
rs13160767	0.87[AMR][1000 genomes]
rs13173678	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13175165	0.91[AMR][1000 genomes]
rs13178037	0.91[AMR][1000 genomes]
rs13182357	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs1328254	0.88[ASN][1000 genomes]
rs13357429	0.90[CEU][hapmap]
rs13358828	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1511737	0.81[EUR][1000 genomes]
rs1511738	0.81[EUR][1000 genomes]
rs1812936	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2005573	0.81[EUR][1000 genomes]
rs2036901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2036902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs2125456	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2137129	0.81[EUR][1000 genomes]
rs2168920	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2199089	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2199090	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2199092	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2199093	0.81[EUR][1000 genomes]
rs2199098	0.84[AMR][1000 genomes]
rs2199099	0.83[AMR][1000 genomes]
rs2219451	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2219452	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2219453	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2219454	0.87[ASN][1000 genomes]
rs2271236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2352789	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668024	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2883164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28885684	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs303219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35295454	0.93[AMR][1000 genomes]
rs4250105	0.81[AMR][1000 genomes]
rs4250165	0.90[AMR][1000 genomes]
rs4302633	0.95[AMR][1000 genomes]
rs4305678	0.90[AMR][1000 genomes]
rs4308516	0.85[AMR][1000 genomes]
rs4321782	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4379243	0.91[AMR][1000 genomes]
rs4415115	0.91[AMR][1000 genomes]
rs4554275	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs471455	0.84[EUR][1000 genomes]
rs471535	0.95[EUR][1000 genomes]
rs472278	0.93[ASN][1000 genomes]
rs473120	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs481222	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs482120	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs485101	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865519	0.81[EUR][1000 genomes]
rs4865549	0.85[AMR][1000 genomes]
rs4865551	0.87[AMR][1000 genomes]
rs4865567	0.88[AMR][1000 genomes]
rs4865637	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4865698	0.81[EUR][1000 genomes]
rs4865699	0.81[EUR][1000 genomes]
rs4865700	0.81[EUR][1000 genomes]
rs4865728	0.86[AMR][1000 genomes]
rs4865761	0.80[AMR][1000 genomes]
rs4865778	0.90[AMR][1000 genomes]
rs4865799	0.82[AMR][1000 genomes]
rs4865801	0.90[AMR][1000 genomes]
rs4866006	0.84[EUR][1000 genomes]
rs494540	0.84[EUR][1000 genomes]
rs496108	0.96[ASN][1000 genomes]
rs498951	0.97[ASN][1000 genomes]
rs5011669	0.81[EUR][1000 genomes]
rs504520	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs506817	0.81[ASN][1000 genomes]
rs507396	0.88[ASN][1000 genomes]
rs527170	0.96[ASN][1000 genomes]
rs528968	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs530430	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs531198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs534123	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535100	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs535113	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs547563	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs552892	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs553798	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs560861	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs561028	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs564641	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs577482	0.84[ASN][1000 genomes]
rs6868721	1.00[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap]
rs72768421	0.85[ASN][1000 genomes]
rs7293304	0.92[AMR][1000 genomes]
rs7293339	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7293348	0.95[AMR][1000 genomes]
rs7293351	0.89[AMR][1000 genomes]
rs7293378	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7293410	0.91[AMR][1000 genomes]
rs7293414	0.92[AMR][1000 genomes]
rs7293426	0.80[ASN][1000 genomes]
rs7293432	0.89[AMR][1000 genomes]
rs7293476	0.90[AMR][1000 genomes]
rs7293501	0.80[AMR][1000 genomes]
rs7447926	0.81[EUR][1000 genomes]
rs7712849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8185119	0.91[AMR][1000 genomes]
rs8185347	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8188005	0.87[AMR][1000 genomes]
rs8188088	0.88[ASN][1000 genomes]
rs8188146	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8188195	0.91[AMR][1000 genomes]
rs8188210	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8188289	0.91[AMR][1000 genomes]
rs9688065	0.88[AMR][1000 genomes]
rs9688258	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:41 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv820439	chr5:49405763-49552643	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	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
3	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
4	nsv598089	chr5:49441601-49547088	ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598091	chr5:49441966-49547088	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv830285	chr5:49445361-49527825	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv598093	chr5:49455285-49547088	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1029710	chr5:49455624-49526015	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1034318	chr5:49455624-49542837	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1028131	chr5:49455624-49552686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1017682	chr5:49455624-49556126	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1033820	chr5:49455624-49560281	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	nsv598095	chr5:49462228-49536268	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv598096	chr5:49462228-49547088	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv598097	chr5:49468722-49549410	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv598098	chr5:49479708-49525181	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv598099	chr5:49479708-49549410	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv598100	chr5:49486237-49525181	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
34	nsv598101	chr5:49492838-49536268	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv598102	chr5:49492838-49547088	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv598103	chr5:49499290-49538362	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv598104	chr5:49499290-49547088	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv598105	chr5:49503299-49547088	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
39	nsv598106	chr5:49507498-49549410	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
40	esv3425783	chr5:49519095-49526793	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
41	esv3412777	chr5:49519095-49526893	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs559096	EMB	cis	parietal	SCAN
rs559096	EMB	cis	Thyroid	GTEx
rs559096	EMB	cis	Whole Blood	GTEx
rs559096	ARL15	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49519800-49524200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:49520600-49525000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:49520600-49526200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
4	chr5:49520600-49527000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr5:49520800-49526000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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