Variant report

Variant	rs11140350
Chromosome Location	chr9:86676854-86676855
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10746731	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780646	0.80[EUR][1000 genomes];0.88[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	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv614762	chr9:86625243-86700593	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1045322	chr9:86666993-86701912	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11140350	C9orf64	cis	cerebellum	SCAN
rs11140350	FRMD3	cis	parietal	SCAN
rs11140350	ISCA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86673400-86677000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr9:86676400-86677200	Enhancers	Colon Smooth Muscle	Colon
3	chr9:86676400-86677200	Enhancers	Psoas Muscle	Psoas
4	chr9:86676400-86677200	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr9:86676400-86677400	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr9:86676400-86678600	Enhancers	Stomach Mucosa	stomach
7	chr9:86676400-86679200	Enhancers	Fetal Heart	heart
8	chr9:86676600-86677600	Enhancers	Fetal Muscle Leg	muscle
9	chr9:86676600-86678600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr9:86676800-86677200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	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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