Variant report

Variant	rs2079138
Chromosome Location	chr7:27115282-27115283
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27114320..27116301-chr7:27117400..27118958,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10238645	0.83[EUR][1000 genomes]
rs10242754	0.94[CEU][hapmap]
rs11563327	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs17471061	0.80[EUR][1000 genomes]
rs17471088	0.86[EUR][1000 genomes]
rs2248744	0.95[CEU][hapmap]
rs2253415	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs2264802	0.82[EUR][1000 genomes]
rs2428416	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2428417	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2428421	0.90[EUR][1000 genomes]
rs2428425	0.97[EUR][1000 genomes]
rs2462900	0.81[EUR][1000 genomes]
rs2462906	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2462908	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2465264	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2465266	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2465274	0.96[EUR][1000 genomes]
rs2522825	0.98[EUR][1000 genomes]
rs2522826	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2648076	0.81[EUR][1000 genomes]
rs2693659	0.90[EUR][1000 genomes]
rs2693665	1.00[CEU][hapmap]
rs2693668	0.82[EUR][1000 genomes]
rs2712234	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2712238	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2712242	0.83[CEU][hapmap]
rs2712246	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2712248	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55889667	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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 miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2079138	HOXA2	cis	Whole Blood	GTEx
rs2079138	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27105800-27118800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:27113200-27118400	Weak transcription	NHEK	skin

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