Variant report

Variant	rs12992042
Chromosome Location	chr2:186506730-186506731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10165430	0.91[EUR][1000 genomes]
rs10185794	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10188730	0.86[EUR][1000 genomes]
rs10196025	0.85[ASN][1000 genomes]
rs10199557	0.83[ASN][1000 genomes]
rs10206949	0.85[ASN][1000 genomes]
rs10210704	0.83[ASN][1000 genomes]
rs10803992	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10803993	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931188	0.91[ASN][1000 genomes]
rs1116941	0.87[ASN][1000 genomes]
rs11688628	0.83[EUR][1000 genomes]
rs11696052	0.88[EUR][1000 genomes]
rs11886336	0.97[ASN][1000 genomes]
rs11893212	0.86[EUR][1000 genomes]
rs12105970	0.88[ASN][1000 genomes]
rs12464911	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12475752	0.86[ASN][1000 genomes]
rs12475908	0.86[ASN][1000 genomes]
rs12988839	0.88[ASN][1000 genomes]
rs12999848	0.86[ASN][1000 genomes]
rs13028347	0.83[ASN][1000 genomes]
rs13393941	0.85[ASN][1000 genomes]
rs1468956	0.89[ASN][1000 genomes]
rs16826958	0.97[ASN][1000 genomes]
rs16827102	0.82[EUR][1000 genomes]
rs2111710	0.83[EUR][1000 genomes]
rs2111711	0.88[ASN][1000 genomes]
rs2216402	0.91[ASN][1000 genomes]
rs2370396	0.81[EUR][1000 genomes]
rs2887742	0.85[ASN][1000 genomes]
rs35740220	0.81[ASN][1000 genomes]
rs36035600	0.88[ASN][1000 genomes]
rs36114949	0.86[ASN][1000 genomes]
rs4233785	0.87[ASN][1000 genomes]
rs4300794	0.87[ASN][1000 genomes]
rs4319900	0.83[ASN][1000 genomes]
rs4377305	0.85[ASN][1000 genomes]
rs4473352	0.90[EUR][1000 genomes]
rs4549042	0.85[ASN][1000 genomes]
rs4666688	0.88[ASN][1000 genomes]
rs4667042	0.86[EUR][1000 genomes]
rs4667044	0.86[ASN][1000 genomes]
rs4667045	0.87[ASN][1000 genomes]
rs4667047	0.91[ASN][1000 genomes]
rs4667051	0.86[ASN][1000 genomes]
rs58762332	0.86[EUR][1000 genomes]
rs6434131	0.83[EUR][1000 genomes]
rs6434134	0.88[ASN][1000 genomes]
rs6434137	0.87[ASN][1000 genomes]
rs6725306	0.87[ASN][1000 genomes]
rs6725553	0.87[ASN][1000 genomes]
rs6729201	0.94[ASN][1000 genomes]
rs6737269	0.86[ASN][1000 genomes]
rs6745292	0.87[ASN][1000 genomes]
rs6749577	0.97[ASN][1000 genomes]
rs6749812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6753011	0.88[ASN][1000 genomes]
rs72898038	0.82[EUR][1000 genomes]
rs7560513	0.87[ASN][1000 genomes]
rs7577283	0.86[EUR][1000 genomes]
rs7577958	0.87[ASN][1000 genomes]
rs7591127	0.86[EUR][1000 genomes]
rs7593254	0.87[ASN][1000 genomes]
rs759686	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs759687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7601391	0.83[ASN][1000 genomes]
rs7604780	0.90[EUR][1000 genomes]
rs763330	0.89[ASN][1000 genomes]
rs984988	0.87[ASN][1000 genomes]
rs988937	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004048	chr2:186303297-186541503	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875540	chr2:186345148-186583961	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv875541	chr2:186345148-186598526	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006219	chr2:186352780-186524793	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv584017	chr2:186352959-186515328	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584018	chr2:186352959-186598526	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv916442	chr2:186356363-186534152	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1000814	chr2:186391490-186520872	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1007052	chr2:186441382-186864390	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv584019	chr2:186445393-186866874	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1000561	chr2:186450293-186556017	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv1009118	chr2:186450293-186864390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1004422	chr2:186463915-186556017	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv2763034	chr2:186473461-186587890	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1008230	chr2:186474069-186818718	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv536076	chr2:186474069-186818718	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv584020	chr2:186475590-186661567	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv584021	chr2:186475590-186866841	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	esv3329661	chr2:186505557-186507705	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12992042	AC007966.1	cis	Adipose Subcutaneous	GTEx
rs12992042	AC007966.1	cis	Thyroid	GTEx
rs12992042	AC007966.1	cis	Esophagus Muscularis	GTEx
rs12992042	AC007966.1	cis	Heart Left Ventricle	GTEx
rs12992042	AC007966.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12992042	AC007966.1	cis	Nerve Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186503800-186508200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:186504200-186509000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:186505400-186508400	Weak transcription	Fetal Stomach	stomach

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