Variant report

Variant	rs13028369
Chromosome Location	chr2:212360399-212360400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10932377	0.91[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10932378	0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11901429	1.00[ASN][1000 genomes]
rs12052273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12052288	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12052398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12053015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12053361	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12105797	0.91[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs12105807	0.91[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs12620169	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12621088	0.91[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs12988861	0.85[ASN][1000 genomes]
rs12989342	0.91[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs12989448	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13003469	0.84[ASN][1000 genomes]
rs13003758	0.84[ASN][1000 genomes]
rs13005140	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs13010155	0.91[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs13028321	1.00[ASN][1000 genomes]
rs13032896	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1851186	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1851189	0.85[CHB][hapmap]
rs2030457	0.80[CHD][hapmap]
rs2030459	0.80[CHD][hapmap]
rs34672401	0.84[ASN][1000 genomes]
rs34777036	0.99[ASN][1000 genomes]
rs34856830	0.88[ASN][1000 genomes]
rs34940919	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35085917	0.84[ASN][1000 genomes]
rs35145864	1.00[ASN][1000 genomes]
rs35234212	0.99[ASN][1000 genomes]
rs35785239	0.89[ASN][1000 genomes]
rs4131610	0.91[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4233983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4233984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4305210	0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4358067	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs4561599	0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4616415	0.93[ASN][1000 genomes]
rs4640327	0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4672615	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4672616	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672617	0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs4672618	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4673621	0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs5028311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6435629	0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs67141123	0.98[ASN][1000 genomes]
rs6741097	0.81[ASN][1000 genomes]
rs6746949	0.91[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs6751135	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000722	chr2:212272622-212465143	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv875778	chr2:212297838-212360994	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv460067	chr2:212313400-212378242	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv584317	chr2:212313400-212378242	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2753335	chr2:212322858-212424019	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv875779	chr2:212340740-212415948	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv875780	chr2:212350245-212415948	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1010811	chr2:212350641-212416215	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv584318	chr2:212351667-212412738	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv528570	chr2:212351667-212413675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv875781	chr2:212351667-212418110	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv470512	chr2:212351667-212428192	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv999487	chr2:212352672-212414582	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv1013164	chr2:212352672-212416215	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv460068	chr2:212355500-212428192	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv584319	chr2:212355500-212428192	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	esv2830116	chr2:212356992-212407077	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13028369	IDH1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:212352800-212362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:212353000-212363400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:212359200-212363200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:212359400-212363200	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links