Variant report

Variant	rs718079
Chromosome Location	chr17:46709835-46709836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1057201	0.98[AFR][1000 genomes]
rs11649801	0.88[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11652932	0.82[MKK][hapmap]
rs11652981	0.82[MKK][hapmap]
rs12942096	0.85[AFR][1000 genomes]
rs2326017	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3744772	0.95[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793596	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs731748	0.97[AFR][1000 genomes]
rs8071699	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap]
rs890435	0.94[ASW][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
2	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
3	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
4	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
5	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
6	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
7	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
8	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
9	nsv543380	chr17:46686151-46721371	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs718079	TTLL6	cis	cerebellum	SCAN
rs718079	GRN	cis	cerebellum	SCAN
rs718079	PNPO	cis	parietal	SCAN
rs718079	RPS5	trans	parietal	SCAN
rs718079	HOXB2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46707600-46710400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
2	chr17:46708200-46710400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:46708400-46712200	Bivalent/Poised TSS	Colonic Mucosa	Colon
4	chr17:46709000-46710000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr17:46709400-46710800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr17:46709600-46710200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr17:46709600-46712200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
8	chr17:46709800-46710000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr17:46709800-46710000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:46709800-46710000	Enhancers	GM12878-XiMat	blood
11	chr17:46709800-46710400	Flanking Active TSS	K562	blood
12	chr17:46709800-46710800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr17:46709800-46711000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
14	chr17:46709800-46711600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:46709800-46712200	Weak transcription	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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