Variant report

Variant	rs6488297
Chromosome Location	chr12:10666025-10666026
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10743908	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10772313	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11836564	0.85[EUR][1000 genomes]
rs16915265	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16915318	0.95[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17206822	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17206857	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17741632	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17741638	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17809278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417907	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34783083	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4620802	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4763544	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55658101	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55693758	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55776135	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55777152	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55791361	0.81[AFR][1000 genomes]
rs55818475	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55922148	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55924876	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55936935	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55962548	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56099735	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56259905	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56377422	0.91[ASN][1000 genomes]
rs56386466	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59007580	0.85[EUR][1000 genomes]
rs59466049	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488298	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488299	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488300	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488301	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67059753	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67181611	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67755400	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67968014	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7134067	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135046	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73054404	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054406	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054408	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054412	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054415	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054418	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054421	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054423	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73054440	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73054441	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73054443	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73054450	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73054466	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73054470	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73054471	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73060470	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73060473	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73060478	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73060482	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73062509	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73062510	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73062511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73062514	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070518	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070521	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070549	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070550	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070554	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070573	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73070576	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73070578	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73070593	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73070596	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73070602	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73072005	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73072007	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73072076	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73072078	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7486108	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7954153	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7955992	0.94[CEU][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7956981	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7966231	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7972425	0.87[EUR][1000 genomes]
rs7977513	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557456	chr12:10532326-10698255	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv898764	chr12:10537269-10698255	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv898765	chr12:10537269-10701992	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv898766	chr12:10537269-10722585	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv557457	chr12:10545925-10698255	Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv557458	chr12:10546140-10698255	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv557459	chr12:10560591-10729821	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv557477	chr12:10601690-10698255	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv557478	chr12:10604945-10698255	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv898772	chr12:10622047-10722585	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv557479	chr12:10644663-10729821	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1042090	chr12:10646985-10695398	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv898773	chr12:10660850-10722585	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv898774	chr12:10666025-10722585	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6488297	CDK9	cis	Frontal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10665000-10666200	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links