Variant report

Variant	rs2712235
Chromosome Location	chr7:27125021-27125022
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	chr7:26902478..26904653-chr7:27124050..27125982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000005020	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1005977	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10231265	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs10267442	0.91[EUR][1000 genomes]
rs1082313	0.82[EUR][1000 genomes]
rs11975480	0.88[EUR][1000 genomes]
rs12673984	0.94[AFR][1000 genomes]
rs12700785	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs17500459	0.81[AFR][1000 genomes]
rs2015424	0.91[EUR][1000 genomes]
rs2252947	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2264680	0.86[EUR][1000 genomes]
rs2428420	0.89[EUR][1000 genomes]
rs2428424	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2428426	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2428427	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2428428	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2428430	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2462901	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2462903	0.89[EUR][1000 genomes]
rs2462905	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462907	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2465263	1.00[CEU][hapmap]
rs2465265	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2465267	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2522822	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2522823	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2522829	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2693658	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2693666	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2712231	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2712232	0.93[EUR][1000 genomes]
rs2712240	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2712241	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2712243	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712249	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936426	0.80[EUR][1000 genomes]
rs2960786	0.80[EUR][1000 genomes]
rs6953314	0.94[AFR][1000 genomes]
rs774248	0.81[EUR][1000 genomes]
rs774254	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs774255	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs774264	0.92[CEU][hapmap]
rs7797624	0.81[AFR][1000 genomes]
rs799237	0.96[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
6	nsv824038	chr7:27119294-27284522	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription 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	183 gene(s)	inside rSNPs	diseases
7	nsv887857	chr7:27120689-27229549	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv824039	chr7:27121825-27294951	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
9	nsv824040	chr7:27121870-27295010	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription 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	183 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2712235	HOXA2	cis	Whole Blood	GTEx
rs2712235	HOTAIRM1	cis	Whole Blood	GTEx
rs2712235	HOXA-AS2	cis	Whole Blood	GTEx
rs2712235	SKAP2	cis	Whole Blood	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27119200-27127600	Weak transcription	Osteobl	bone
2	chr7:27122600-27127400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:27122800-27133600	Weak transcription	HMEC	breast
4	chr7:27125000-27125200	Active TSS	Sigmoid Colon	Sigmoid Colon

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