Variant report

Variant	rs6560510
Chromosome Location	chr9:78923351-78923352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11788518	0.85[ASN][1000 genomes]
rs17721191	0.85[ASN][1000 genomes]
rs1845639	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2351466	0.88[ASN][1000 genomes]
rs72743110	0.85[ASN][1000 genomes]
rs7850408	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv3337929	chr9:78917532-78923930	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
6	esv3481660	chr9:78918557-78923505	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv435888	chr9:78919188-78924556	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv526457	chr9:78923257-78924848	Strong transcription Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6560510	RFK	cis	cerebellum	SCAN
rs6560510	C9orf95	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78912400-78927800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:78913400-78935200	Weak transcription	Small Intestine	intestine
3	chr9:78916000-78925400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr9:78917400-78928000	Weak transcription	Colonic Mucosa	Colon
5	chr9:78917600-78923600	Weak transcription	Fetal Intestine Large	intestine
6	chr9:78918800-78924000	Weak transcription	Fetal Intestine Small	intestine
7	chr9:78919000-78924800	Weak transcription	Placenta	Placenta
8	chr9:78922600-78925600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:78922600-78953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:78922800-78923400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr9:78923000-78923800	Enhancers	Stomach Mucosa	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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