Variant report

Variant	rs11130183
Chromosome Location	chr3:49228946-49228947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49227118..49229185-chr3:49314324..49316369,3	K562	blood:

Variant related genes	Relation type
ENSG00000188315	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 31 )

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

rs_ID	r²[population]
rs10154992	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11719762	0.95[CEU][hapmap]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs12637346	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13084037	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082923	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099526	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3448	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs35713889	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4292260	0.81[ASW][hapmap];0.87[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs4384984	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955411	0.81[ASW][hapmap];0.87[CEU][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs4955414	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955416	0.81[ASW][hapmap];0.82[CEU][hapmap];0.85[YRI][hapmap]
rs4955417	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4955421	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955426	0.87[CEU][hapmap]
rs4955427	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955439	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974081	0.82[CEU][hapmap]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs6446204	0.82[CEU][hapmap]
rs6446256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772452	0.82[CEU][hapmap]
rs6778080	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6787808	0.82[CEU][hapmap]
rs6798112	0.85[CEU][hapmap]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809851	0.95[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7429661	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432077	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7434187	0.82[CEU][hapmap]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974495	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9865051	0.87[CEU][hapmap]
rs9867285	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.95[CEU][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs11130183	NICN1-AS1	cis	Thyroid	GTEx
rs11130183	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs11130183	WDR6	cis	Heart Left Ventricle	GTEx
rs11130183	NICN1	cis	cerebellum	SCAN
rs11130183	SEMA3G	cis	cerebellum	SCAN
rs11130183	ARIH2	cis	Thyroid	GTEx
rs11130183	WDR6	cis	Muscle Skeletal	GTEx
rs11130183	AMT	cis	Whole Blood	GTEx
rs11130183	GMPPB	cis	parietal	SCAN
rs11130183	AMT	cis	Adipose Subcutaneous	GTEx
rs11130183	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs11130183	QRICH1	cis	cerebellum	SCAN
rs11130183	AMT	cis	Muscle Skeletal	GTEx
rs11130183	AMT	cis	Thyroid	GTEx
rs11130183	AMT	cis	cerebellum	SCAN
rs11130183	DALRD3	cis	cerebellum	SCAN
rs11130183	NICN1	cis	Thyroid	GTEx
rs11130183	WDR6	cis	parietal	SCAN
rs11130183	GPX1	cis	parietal	SCAN
rs11130183	AMT	cis	lung	GTEx
rs11130183	AMT	cis	Artery Aorta	GTEx
rs11130183	WDR6	cis	Nerve Tibial	GTEx
rs11130183	AMT	cis	Artery Tibial	GTEx
rs11130183	AMT	cis	Esophagus Mucosa	GTEx
rs11130183	P4HTM	cis	parietal	SCAN
rs11130183	PFKFB4	cis	Nerve Tibial	GTEx
rs11130183	AMT	cis	Nerve Tibial	GTEx
rs11130183	DALRD3	cis	parietal	SCAN
rs11130183	WDR6	cis	cerebellum	SCAN
rs11130183	ZNF589	cis	parietal	SCAN
rs11130183	AMT	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49215600-49229000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:49216200-49236400	Weak transcription	Esophagus	oesophagus
3	chr3:49228400-49230200	Enhancers	Fetal Heart	heart
4	chr3:49228600-49229600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49228600-49229600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:49228600-49229600	Enhancers	HepG2	liver
7	chr3:49228600-49230200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:49228800-49229200	Enhancers	Right Ventricle	heart
9	chr3:49228800-49229200	Enhancers	NHEK	skin
10	chr3:49228800-49229400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:49228800-49236400	Weak transcription	Right Atrium	heart

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