Variant report

Variant	rs12079099
Chromosome Location	chr1:152494966-152494967
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	chr1:152494849..152497210-chr1:152499471..152502246,2	MCF-7	breast:
2	chr1:152486736..152490871-chr1:152492622..152496834,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169509	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1001833	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205011	0.85[AMR][1000 genomes]
rs11205013	0.85[AMR][1000 genomes]
rs11205015	1.00[AMR][1000 genomes]
rs11205016	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205021	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081449	0.85[AMR][1000 genomes]
rs12083339	1.00[AMR][1000 genomes]
rs12091397	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097074	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1337339	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1337343	1.00[AMR][1000 genomes]
rs1361061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834165	1.00[AMR][1000 genomes]
rs16834172	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834179	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1819602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1856122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4573527	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6674436	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6695861	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73004851	1.00[AMR][1000 genomes]
rs73004866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73004867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73004887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73006961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73006963	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73006967	0.87[AMR][1000 genomes]
rs7526623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7538262	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7541949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7542704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7549858	0.85[AMR][1000 genomes]
rs945787	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2750810	chr1:152453669-152660927	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1012908	chr1:152464844-152517845	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1005553	chr1:152464844-152519197	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1013357	chr1:152469744-152519184	Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1798404	chr1:152472839-152587113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv1827111	chr1:152472839-152690073	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv1830764	chr1:152472839-152690073	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv518413	chr1:152488428-152497685	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152493400-152496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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