Variant report

Variant	rs12519532
Chromosome Location	chr5:42829303-42829304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42825774..42827829-chr5:42829137..42831240,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250722	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs1035516	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1046068	0.91[CEU][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs10462041	0.96[EUR][1000 genomes]
rs1074263	0.88[ASN][1000 genomes]
rs10941586	0.81[EUR][1000 genomes]
rs10941587	0.97[EUR][1000 genomes]
rs10941591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10941592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10941593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11952526	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11953691	0.81[EUR][1000 genomes]
rs11957181	0.81[EUR][1000 genomes]
rs11958761	0.81[AMR][1000 genomes]
rs12054838	0.92[EUR][1000 genomes]
rs12055087	0.86[EUR][1000 genomes]
rs12055266	0.97[EUR][1000 genomes]
rs12187466	0.81[EUR][1000 genomes]
rs12187996	0.91[CEU][hapmap];0.92[YRI][hapmap]
rs12516157	0.86[EUR][1000 genomes]
rs12516954	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12517008	0.89[ASN][1000 genomes]
rs12517112	0.91[CEU][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs12518414	0.90[EUR][1000 genomes]
rs12519443	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12521615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167366	0.87[CHB][hapmap];0.96[JPT][hapmap];0.90[ASN][1000 genomes]
rs13178745	0.99[EUR][1000 genomes]
rs1345824	0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1345825	0.87[ASN][1000 genomes]
rs1364024	0.90[EUR][1000 genomes]
rs1364026	0.86[EUR][1000 genomes]
rs1364027	0.96[EUR][1000 genomes]
rs1423653	0.88[ASN][1000 genomes]
rs1423654	0.86[EUR][1000 genomes]
rs1423656	0.82[ASN][1000 genomes]
rs1593070	0.86[EUR][1000 genomes]
rs1593071	0.88[ASN][1000 genomes]
rs1862628	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1862629	0.90[ASN][1000 genomes]
rs1862630	0.91[CHB][hapmap];0.96[JPT][hapmap]
rs1895457	0.88[ASN][1000 genomes]
rs2014958	0.88[ASN][1000 genomes]
rs2113086	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2113088	0.88[ASN][1000 genomes]
rs2161600	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs230807	0.88[ASN][1000 genomes]
rs230812	0.90[ASN][1000 genomes]
rs230813	0.90[ASN][1000 genomes]
rs230814	0.88[ASN][1000 genomes]
rs230816	0.89[ASN][1000 genomes]
rs230819	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs230820	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2459629	0.88[ASN][1000 genomes]
rs28919269	0.87[EUR][1000 genomes]
rs28919892	0.91[CEU][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs28919916	0.87[EUR][1000 genomes]
rs2910851	0.88[ASN][1000 genomes]
rs2910855	0.88[ASN][1000 genomes]
rs2910856	0.88[ASN][1000 genomes]
rs2910862	0.88[ASN][1000 genomes]
rs2910864	0.88[ASN][1000 genomes]
rs2910871	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2910875	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2910880	0.90[ASN][1000 genomes]
rs2910881	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2972756	0.90[ASN][1000 genomes]
rs2972757	0.90[ASN][1000 genomes]
rs2972758	0.87[ASN][1000 genomes]
rs2972759	0.90[ASN][1000 genomes]
rs2972761	0.90[ASN][1000 genomes]
rs2972763	0.90[ASN][1000 genomes]
rs2972767	0.88[ASN][1000 genomes]
rs2972783	0.88[ASN][1000 genomes]
rs2972992	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2972994	0.91[CHB][hapmap];0.96[JPT][hapmap]
rs2972998	0.88[ASN][1000 genomes]
rs2972999	0.88[ASN][1000 genomes]
rs2973000	0.88[ASN][1000 genomes]
rs2973001	0.88[ASN][1000 genomes]
rs2973006	0.88[ASN][1000 genomes]
rs2973011	0.88[ASN][1000 genomes]
rs2973015	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2973018	0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2973023	0.86[ASN][1000 genomes]
rs2973028	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2973029	0.88[ASN][1000 genomes]
rs34443829	0.96[ASN][1000 genomes]
rs34926728	0.95[ASN][1000 genomes]
rs35293842	0.89[ASN][1000 genomes]
rs3797310	0.85[EUR][1000 genomes]
rs3797311	0.85[EUR][1000 genomes]
rs3866438	0.86[EUR][1000 genomes]
rs3870358	0.86[EUR][1000 genomes]
rs3870359	0.86[EUR][1000 genomes]
rs3906418	0.97[EUR][1000 genomes]
rs4143864	0.87[EUR][1000 genomes]
rs4242120	0.81[EUR][1000 genomes]
rs4242121	0.81[EUR][1000 genomes]
rs4866797	0.81[EUR][1000 genomes]
rs4866798	0.86[EUR][1000 genomes]
rs4866799	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4866800	0.87[CHB][hapmap];0.96[JPT][hapmap];0.91[ASN][1000 genomes]
rs4866801	0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4866802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4866949	0.90[CEU][hapmap];0.90[YRI][hapmap]
rs4866954	0.81[EUR][1000 genomes]
rs4866958	0.86[EUR][1000 genomes]
rs4866959	0.86[EUR][1000 genomes]
rs4866961	0.97[EUR][1000 genomes]
rs4866962	0.86[EUR][1000 genomes]
rs4866963	0.86[EUR][1000 genomes]
rs4866966	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4866967	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55651065	0.97[EUR][1000 genomes]
rs55660133	0.90[EUR][1000 genomes]
rs55687632	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55688895	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56273800	0.86[EUR][1000 genomes]
rs56394865	0.97[EUR][1000 genomes]
rs56848171	0.81[EUR][1000 genomes]
rs58429632	0.86[EUR][1000 genomes]
rs59184964	0.89[EUR][1000 genomes]
rs60008560	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6180	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs62370873	0.81[EUR][1000 genomes]
rs62370874	0.81[EUR][1000 genomes]
rs62370911	0.86[EUR][1000 genomes]
rs62370912	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62370950	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62370951	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62370952	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62370953	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62370955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62372042	0.81[EUR][1000 genomes]
rs6865453	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6875431	0.91[YRI][hapmap]
rs6882333	0.87[CHB][hapmap];0.96[JPT][hapmap];0.90[ASN][1000 genomes]
rs6886900	0.91[YRI][hapmap]
rs6889614	0.92[YRI][hapmap]
rs6899268	0.86[EUR][1000 genomes]
rs719756	0.86[ASN][1000 genomes]
rs722678	0.81[EUR][1000 genomes]
rs7579	0.87[CEU][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs7708223	0.91[CEU][hapmap];0.91[YRI][hapmap]
rs7708337	0.85[EUR][1000 genomes]
rs7725776	0.91[CEU][hapmap];0.92[YRI][hapmap]
rs7725961	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7734918	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs8180394	0.86[EUR][1000 genomes]
rs8180482	0.97[EUR][1000 genomes]
rs9637794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription 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	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
14	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
15	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
16	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12519532	SEPP1	Cis_1M	lymphoblastoid	RTeQTL
rs12519532	CCDC152	cis	Artery Aorta	GTEx
rs12519532	CCDC152	cis	Artery Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42826000-42830600	Enhancers	Fetal Stomach	stomach
2	chr5:42826400-42830000	Enhancers	HepG2	liver
3	chr5:42828800-42829800	Enhancers	Fetal Lung	lung
4	chr5:42829000-42829400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr5:42829000-42829800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:42829200-42829400	Enhancers	Placenta	Placenta

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