Variant report

Variant	rs4877709
Chromosome Location	chr9:85400266-85400267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11139750	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11139751	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11139766	0.82[EUR][1000 genomes]
rs11139788	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12551526	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13284468	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13290181	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1998302	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1998304	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34934271	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35933972	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4877235	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4877705	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62576976	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428539	chr9:85240027-85402367	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1035314	chr9:85348780-85549246	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv540161	chr9:85348780-85549246	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1039930	chr9:85349993-85536746	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4877709	ADH4	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85390800-85400600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
2	chr9:85391600-85404000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:85393400-85403800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:85395400-85401400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:85395400-85424800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:85398400-85400400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:85399600-85404400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:85399800-85404200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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