Variant report

Variant	rs477924
Chromosome Location	chr7:26854554-26854555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26843884..26846440-chr7:26852845..26855435,2	MCF-7	breast:
2	chr7:26853916..26855656-chr7:26857931..26859588,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1391805	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs213515	0.94[CEU][hapmap]
rs213516	0.82[CEU][hapmap]
rs213525	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213528	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs213533	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213536	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2140998	0.81[CEU][hapmap]
rs471536	1.00[JPT][hapmap]
rs490366	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs514043	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs550141	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs558263	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564260	1.00[JPT][hapmap]
rs591895	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs640512	1.00[JPT][hapmap];0.86[YRI][hapmap]
rs659131	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs668052	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs673502	1.00[JPT][hapmap]
rs688039	1.00[JPT][hapmap]
rs774252	0.88[CEU][hapmap]
rs774265	0.94[CEU][hapmap]
rs7791056	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv887855	chr7:26823963-26872652	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs477924	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26808000-26854800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:26839400-26871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:26843600-26870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:26843600-26871400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:26843800-26863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:26850000-26869200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:26850200-26861800	Weak transcription	Primary B cells from cord blood	blood
10	chr7:26850200-26862600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:26850400-26862600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr7:26850400-26863400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr7:26850400-26871400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr7:26851800-26855800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:26852600-26870600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:26853000-26855600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr7:26853400-26882600	Weak transcription	Adipose Nuclei	Adipose
18	chr7:26853600-26855200	Weak transcription	Brain Germinal Matrix	brain
19	chr7:26853600-26872000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:26853800-26856200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:26853800-26871400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:26854200-26855600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:26854200-26876400	Weak transcription	Fetal Lung	lung

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