Variant report

Variant	rs976825
Chromosome Location	chr9:78928591-78928592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1817915	0.88[EUR][1000 genomes]
rs2055164	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2490591	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2643333	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2643334	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs924013	0.83[AMR][1000 genomes];0.86[EUR][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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv508552	chr9:78864913-78956326	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv893477	chr9:78892526-78932928	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs976825	GNAQ	cis	parietal	SCAN
rs976825	TMC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78913400-78935200	Weak transcription	Small Intestine	intestine
2	chr9:78922600-78953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:78927200-78928600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:78927200-78930800	Weak transcription	Fetal Intestine Large	intestine
5	chr9:78927400-78929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:78927400-78930200	Weak transcription	Placenta	Placenta
7	chr9:78927800-78929000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:78927800-78929200	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr9:78927800-78929400	Enhancers	Stomach Mucosa	stomach
10	chr9:78928200-78928600	Weak transcription	Colonic Mucosa	Colon
11	chr9:78928200-78929800	Genic enhancers	Fetal Intestine Small	intestine
12	chr9:78928400-78929000	Enhancers	Rectal Mucosa Donor 31	rectum

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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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