Variant report

Variant	rs7468504
Chromosome Location	chr9:92925179-92925180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10820972	0.88[ASN][1000 genomes]
rs10992311	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10992324	0.88[ASN][1000 genomes]
rs10992326	0.86[ASN][1000 genomes]
rs28571209	0.87[ASN][1000 genomes]
rs28680232	0.84[ASN][1000 genomes]
rs28820642	0.88[ASN][1000 genomes]
rs56822056	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7025302	0.86[YRI][hapmap]
rs7037744	0.86[YRI][hapmap]
rs9785239	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[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	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv893563	chr9:92816727-92967125	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1051180	chr9:92869383-93141038	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv540169	chr9:92869383-93141038	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482531	chr9:92907692-93096360	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3321749	chr9:92922632-92927130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3381666	chr9:92923132-92926430	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3377946	chr9:92923332-92926330	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7468504	FGD3	cis	cerebellum	SCAN
rs7468504	GOLM1	cis	parietal	SCAN
rs7468504	SEMA4D	cis	parietal	SCAN
rs7468504	SPIN1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92923800-92925200	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr9:92923800-92925600	Enhancers	Primary B cells from peripheral blood	blood
3	chr9:92924000-92925200	Enhancers	Spleen	Spleen
4	chr9:92924600-92925200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:92924600-92925200	Enhancers	Esophagus	oesophagus
6	chr9:92924600-92925200	ZNF genes & repeats	Fetal Kidney	kidney
7	chr9:92924600-92925200	Enhancers	Pancreas	Pancrea
8	chr9:92924800-92925400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:92924800-92925600	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr9:92924800-92925600	Enhancers	Stomach Mucosa	stomach
11	chr9:92924800-92925800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr9:92925000-92925400	Enhancers	Primary B cells from cord blood	blood
13	chr9:92925000-92925400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr9:92925000-92925600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:92925000-92925600	ZNF genes & repeats	Fetal Intestine Large	intestine
16	chr9:92925000-92928800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:92925000-92929000	Weak transcription	Colonic Mucosa	Colon

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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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