Variant report

Variant	rs16933965
Chromosome Location	chr9:16022561-16022562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10810512	0.85[ASN][1000 genomes]
rs10962251	0.85[ASN][1000 genomes]
rs11790527	0.83[ASN][1000 genomes]
rs11792622	0.85[ASN][1000 genomes]
rs13298860	0.83[AFR][1000 genomes]
rs13298936	0.83[AFR][1000 genomes]
rs17352900	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17353213	0.85[AFR][1000 genomes]
rs3008713	0.88[AFR][1000 genomes]
rs3008714	0.81[AFR][1000 genomes]
rs66532067	0.85[ASN][1000 genomes]
rs7031840	0.85[ASN][1000 genomes]
rs7848880	0.84[AFR][1000 genomes]
rs9407712	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025555	chr9:16022186-16064158	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16933965	C9orf93	cis	cerebellum	SCAN
rs16933965	SNAPC3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16018200-16028600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:16019800-16024400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:16022200-16022600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr9:16022200-16022800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:16022200-16022800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:16022400-16022600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:16022400-16022600	Enhancers	NHLF	lung
8	chr9:16022400-16023000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:16022400-16023000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:16022400-16023600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:16022400-16024200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:16022400-16024800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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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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