Variant report

Variant	rs731007
Chromosome Location	chr7:25560705-25560706
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10242326	0.82[EUR][1000 genomes]
rs1027672	0.90[ASN][1000 genomes]
rs12667972	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12668322	0.82[ASN][1000 genomes]
rs12668343	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12672646	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12673720	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1393675	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17151747	0.80[ASN][1000 genomes]
rs17151750	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17151753	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17151766	0.82[ASN][1000 genomes]
rs17151770	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61238582	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs731008	1.00[ASN][1000 genomes]
rs73275554	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7796244	0.97[AMR][1000 genomes];0.91[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs731007	HOXA9	cis	cerebellum	SCAN
rs731007	CDCA7L	cis	cerebellum	SCAN
rs731007	HOXA3	cis	cerebellum	SCAN
rs731007	CDCA7L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25558800-25562800	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr7:25558800-25563000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr7:25559000-25562200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr7:25559000-25563200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr7:25559000-25563200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr7:25559000-25563400	Enhancers	Primary T cells from cord blood	blood
7	chr7:25559800-25561000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:25560200-25561800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr7:25560400-25563400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr7:25560600-25561800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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

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