Variant report

Variant	rs2428428
Chromosome Location	chr7:27115265-27115266
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	chr7:27114320..27116301-chr7:27117400..27118958,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005977	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10231265	0.93[CEU][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10267442	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1082313	0.83[EUR][1000 genomes]
rs11975480	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13311400	0.81[EUR][1000 genomes]
rs2015424	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213520	0.81[EUR][1000 genomes]
rs2252947	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2264680	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2428420	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2428424	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2428426	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2428427	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2428430	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462901	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2462903	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462905	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462907	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2465263	1.00[CEU][hapmap]
rs2465265	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2465267	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2522822	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2522823	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2522829	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2693658	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2693666	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712231	0.96[CEU][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712232	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712235	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2712240	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2712241	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712243	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2712249	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2936426	0.82[EUR][1000 genomes]
rs2960784	0.81[EUR][1000 genomes]
rs2960786	0.82[EUR][1000 genomes]
rs774248	0.83[EUR][1000 genomes]
rs774254	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs774255	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs774264	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs799237	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2428428	SKAP2	cis	Whole Blood	GTEx
rs2428428	HOTAIRM1	cis	Whole Blood	GTEx
rs2428428	HOXA2	cis	Whole Blood	GTEx
rs2428428	HOXA-AS2	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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