Variant report

Variant	rs2842477
Chromosome Location	chr9:78914023-78914024
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1078868	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2643333	0.81[AMR][1000 genomes]
rs2643334	0.81[AMR][1000 genomes]
rs749836	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs924013	0.81[AMR][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	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
5	esv1010025	chr9:78912186-78922397	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2842477	TMC1	cis	parietal	SCAN
rs2842477	GNAQ	cis	parietal	SCAN
rs2842477	C9orf95	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78883000-78917200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:78903400-78917600	Weak transcription	Stomach Mucosa	stomach
3	chr9:78905800-78922400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:78912000-78916000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr9:78912000-78917600	Strong transcription	Fetal Intestine Large	intestine
6	chr9:78912400-78927800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:78912800-78915200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:78913000-78914200	Enhancers	Fetal Kidney	kidney
9	chr9:78913200-78918000	Weak transcription	Placenta	Placenta
10	chr9:78913400-78914200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr9:78913400-78914200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr9:78913400-78935200	Weak transcription	Small Intestine	intestine
13	chr9:78913600-78915200	Weak transcription	HSMMtube	muscle
14	chr9:78913800-78917400	Strong transcription	Fetal Intestine Small	intestine
15	chr9:78914000-78915000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:78914000-78915000	Weak transcription	Adipose Nuclei	Adipose

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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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