Variant report

Variant	rs11162842
Chromosome Location	chr1:80325187-80325188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10874084	0.81[ASN][1000 genomes]
rs10874088	0.81[ASN][1000 genomes]
rs10874091	0.93[EUR][1000 genomes]
rs11162839	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162840	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11802723	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122162	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12122335	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402955	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12404878	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012286	chr1:80057078-81005153	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv535018	chr1:80057078-81005153	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1000792	chr1:80076146-81015283	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv546638	chr1:80131994-80353796	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1002522	chr1:80210698-80532133	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv997278	chr1:80220617-80479841	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv535019	chr1:80220617-80479841	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1009169	chr1:80220817-80479702	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv535020	chr1:80220817-80479702	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1011192	chr1:80226910-80532133	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1014763	chr1:80231767-80529703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv535021	chr1:80231767-80529703	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv916146	chr1:80289899-80479694	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv462184	chr1:80297950-80731568	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv546645	chr1:80297950-80731568	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv34144	chr1:80321018-80572745	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11162842	RABGGTB	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:80324000-80327000	Enhancers	HUVEC	blood vessel
2	chr1:80324600-80325200	Enhancers	Gastric	stomach
3	chr1:80324600-80325200	Enhancers	Ovary	ovary
4	chr1:80324600-80325800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:80324800-80325200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:80324800-80325200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:80324800-80325200	Enhancers	HMEC	breast
8	chr1:80324800-80325600	Enhancers	NHLF	lung
9	chr1:80324800-80325800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:80324800-80325800	Enhancers	Stomach Mucosa	stomach
11	chr1:80324800-80326000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:80325000-80325200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:80325000-80325200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:80325000-80325400	Enhancers	NH-A	brain
15	chr1:80325000-80325400	Enhancers	NHEK	skin
16	chr1:80325000-80325600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:80325000-80325600	Enhancers	A549	lung
18	chr1:80325000-80326000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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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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