Variant report

Variant	rs1393673
Chromosome Location	chr7:25596372-25596373
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12670768	1.00[MEX][hapmap]
rs16873895	1.00[MEX][hapmap]
rs2938112	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2938113	0.93[EUR][1000 genomes]
rs2960819	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2960821	1.00[MEX][hapmap]
rs2999574	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1393673	HOXA7	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25579800-25600800	Weak transcription	Lung	lung
2	chr7:25589800-25597200	Weak transcription	Ovary	ovary
3	chr7:25594000-25597000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:25594000-25601800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:25595800-25597400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr7:25596000-25596400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:25596000-25596400	Enhancers	Fetal Brain Male	brain
8	chr7:25596000-25596800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:25596000-25597400	Enhancers	Brain Germinal Matrix	brain
10	chr7:25596200-25601600	Weak transcription	Fetal Brain Female	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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