Variant report

Variant	rs11689622
Chromosome Location	chr2:48659678-48659679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48657438..48661343-chr2:48665972..48669898,5	K562	blood:

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10211336	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10454133	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10454134	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10495951	0.87[JPT][hapmap]
rs10495952	0.87[JPT][hapmap];0.89[MEX][hapmap]
rs11125173	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs11679523	0.90[GIH][hapmap];0.87[JPT][hapmap]
rs11680719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11680916	0.86[JPT][hapmap]
rs11683639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11683708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11685861	0.87[JPT][hapmap]
rs11688481	0.90[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap]
rs11690690	0.87[JPT][hapmap]
rs11690748	0.87[JPT][hapmap]
rs11690845	0.86[GIH][hapmap];0.87[JPT][hapmap]
rs13399936	0.97[ASN][1000 genomes]
rs13400909	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13401749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13401752	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17037289	0.87[JPT][hapmap]
rs17037298	0.95[GIH][hapmap];0.87[JPT][hapmap]
rs17855177	0.87[JPT][hapmap]
rs35913553	0.93[EUR][1000 genomes]
rs4131784	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs4274640	0.96[ASN][1000 genomes]
rs4316980	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4344965	0.87[JPT][hapmap]
rs4438532	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4494796	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4547570	0.91[EUR][1000 genomes]
rs4549145	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs4606978	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4638844	0.90[ASN][1000 genomes]
rs55640438	0.92[ASN][1000 genomes]
rs55757090	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55971719	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56156294	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56365822	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58020097	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58969359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58978223	0.82[ASN][1000 genomes]
rs59045263	0.90[EUR][1000 genomes]
rs60042255	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60825643	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60988618	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61303367	0.82[ASN][1000 genomes]
rs62137018	0.83[ASN][1000 genomes]
rs62137019	0.83[ASN][1000 genomes]
rs62137021	0.81[ASN][1000 genomes]
rs62137041	0.92[ASN][1000 genomes]
rs66705539	0.81[ASN][1000 genomes]
rs6705802	0.87[JPT][hapmap]
rs6718068	0.87[JPT][hapmap]
rs6732196	0.89[ASN][1000 genomes]
rs6743757	0.86[JPT][hapmap]
rs6747441	0.91[EUR][1000 genomes]
rs6749773	0.83[ASN][1000 genomes]
rs72820454	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72820474	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820479	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72820484	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72820492	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820494	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72820499	0.97[ASN][1000 genomes]
rs7562069	0.87[JPT][hapmap]
rs7562816	0.87[JPT][hapmap]
rs7565792	0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs7566239	0.87[JPT][hapmap]
rs7576964	0.82[JPT][hapmap]
rs7577237	0.87[JPT][hapmap]
rs7579932	0.86[JPT][hapmap]
rs7600794	0.87[JPT][hapmap]
rs7606104	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11689622	STON1-GTF2A1L	cis	cerebellum	SCAN
rs11689622	PPP1R21	cis	Thyroid	GTEx
rs11689622	FOXN2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48652000-48660200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:48653600-48661200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:48655800-48660800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:48659000-48660000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:48659600-48660000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:48659600-48660600	Enhancers	HepG2	liver

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