Variant report

Variant	rs11080353
Chromosome Location	chr17:33871281-33871282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11080354	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11080355	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11659054	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150450	0.94[CEU][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17550268	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35614987	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66878360	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7501448	0.83[CEU][hapmap]
rs7502331	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8065635	0.82[CEU][hapmap]
rs8070030	0.82[CEU][hapmap]
rs8073060	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9894813	0.82[CEU][hapmap];0.80[TSI][hapmap]

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	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574754	chr17:33841737-33881631	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11080353	C17orf75	cis	cerebellum	SCAN
rs11080353	TBC1D29	cis	cerebellum	SCAN
rs11080353	LOC645744	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33868600-33871600	Enhancers	Primary hematopoietic stem cells	blood
2	chr17:33868600-33871600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:33868600-33872200	Weak transcription	Stomach Mucosa	stomach
4	chr17:33868600-33872200	Weak transcription	A549	lung
5	chr17:33868800-33871400	Enhancers	HUVEC	blood vessel
6	chr17:33869000-33872600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr17:33869000-33873200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr17:33869800-33877200	Weak transcription	Lung	lung
9	chr17:33870400-33881000	Weak transcription	K562	blood
10	chr17:33870400-33888600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr17:33870600-33873200	Weak transcription	GM12878-XiMat	blood
12	chr17:33870800-33871400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr17:33870800-33873200	Weak transcription	Primary B cells from cord blood	blood
14	chr17:33871000-33871600	Enhancers	Dnd41	blood
15	chr17:33871000-33872800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:33871000-33873200	Weak transcription	Adipose Nuclei	Adipose
17	chr17:33871000-33873400	Weak transcription	Primary B cells from peripheral blood	blood

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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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