Variant report

Variant	rs12673984
Chromosome Location	chr7:27122078-27122079
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27120424..27122437-chr7:27131942..27133527,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10257437	0.82[CEU][hapmap]
rs10257464	0.87[CEU][hapmap]
rs10276952	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11977871	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12674308	0.90[ASN][1000 genomes]
rs12700771	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700785	0.94[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13230726	0.89[EUR][1000 genomes]
rs17427218	0.94[ASN][1000 genomes]
rs17436827	0.82[ASN][1000 genomes]
rs17437154	0.94[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs17448911	0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs17500459	0.86[AFR][1000 genomes]
rs213516	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs2259141	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs2301719	0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2693660	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2693661	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2693669	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712235	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs2712249	0.92[AFR][1000 genomes]
rs28357116	0.91[ASN][1000 genomes]
rs62454362	0.91[ASN][1000 genomes]
rs62454371	0.89[ASN][1000 genomes]
rs62454372	0.96[ASN][1000 genomes]
rs62454374	0.96[ASN][1000 genomes]
rs62454375	0.96[ASN][1000 genomes]
rs62457404	0.90[ASN][1000 genomes]
rs6948446	0.94[ASN][1000 genomes]
rs6953314	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706015	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs774249	0.82[ASN][1000 genomes]
rs774250	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs774251	0.82[ASN][1000 genomes]
rs774252	0.82[CEU][hapmap]
rs774253	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs774256	0.80[ASN][1000 genomes]
rs774265	0.81[CEU][hapmap]
rs7791056	0.82[CEU][hapmap]
rs7797624	0.86[AFR][1000 genomes]
rs954051	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12673984	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27118400-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:27118800-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:27118800-27122800	Enhancers	HMEC	breast
4	chr7:27119000-27122600	Enhancers	Hela-S3	cervix
5	chr7:27119200-27127600	Weak transcription	Osteobl	bone
6	chr7:27119600-27125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:27120800-27122600	Enhancers	NHEK	skin
8	chr7:27121000-27122200	Weak transcription	HSMM	muscle
9	chr7:27121200-27122400	Weak transcription	A549	lung
10	chr7:27121400-27122400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:27121800-27122600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:27121800-27122600	Enhancers	Muscle Satellite Cultured Cells	--

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