Variant report

Variant	rs7799519
Chromosome Location	chr7:26699295-26699296
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	chr7:26692789..26695247-chr7:26695644..26699450,4	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1024452	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024453	0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129771	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971041	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971098	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972823	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973332	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976472	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978456	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979611	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982489	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57579189	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57687803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591895	0.81[TSI][hapmap]
rs61609910	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945204	0.83[EUR][1000 genomes]
rs6967749	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970475	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73683491	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683496	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683510	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777645	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780206	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809419	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv830929	chr7:26587888-26749735	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1020378	chr7:26679880-26733872	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7799519	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26678800-26715400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:26679400-26710000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:26680400-26704400	Weak transcription	Primary B cells from cord blood	blood
4	chr7:26685600-26704400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr7:26686400-26701600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr7:26688800-26704400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:26694200-26704000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:26696200-26699400	Enhancers	Placenta	Placenta
9	chr7:26696400-26704400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr7:26696800-26708000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr7:26697600-26700000	Enhancers	Fetal Brain Male	brain
12	chr7:26698200-26699400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:26698200-26699600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:26698200-26703400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:26698400-26699800	Enhancers	Brain Germinal Matrix	brain
16	chr7:26698800-26706800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:26699000-26699800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:26699000-26700200	Enhancers	Fetal Brain Female	brain
19	chr7:26699200-26700200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:26699200-26707000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr7:26699200-26707000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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