Variant report

Variant	rs11712056
Chromosome Location	chr3:49914397-49914398
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	chr3:49839311..49841661-chr3:49914034..49916864,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAMKV-1	chr3:49914090-49914772	NONHSAT089768

Variant related genes	Relation type
ENSG00000185614	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1062633	0.81[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11130222	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs11709573	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713193	0.81[ASN][1000 genomes]
rs11714324	0.90[ASN][1000 genomes]
rs11721204	0.89[ASN][1000 genomes]
rs12496973	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs12634780	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13060128	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs13077403	0.86[ASN][1000 genomes]
rs13079006	0.82[ASN][1000 genomes]
rs13082703	0.83[ASN][1000 genomes]
rs17657664	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs17657688	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs2230590	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2240327	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2240328	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2240329	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2252833	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2280406	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2352969	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2352984	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353579	0.82[JPT][hapmap]
rs2526747	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2526748	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2526751	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2624819	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2624821	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2624822	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2624832	0.83[ASN][1000 genomes]
rs2624843	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2681776	0.83[ASN][1000 genomes]
rs2681779	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2681780	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2681781	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs2777888	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2883057	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2883059	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34034116	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34312088	0.83[ASN][1000 genomes]
rs34654589	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35275715	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36022378	0.98[ASN][1000 genomes]
rs3733134	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774734	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs3774759	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688688	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4688689	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688690	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688753	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4688755	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688758	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs55692411	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62262114	0.82[ASN][1000 genomes]
rs6446193	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6762477	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6765484	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6771546	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6772095	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6774354	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6792892	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6793528	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6795703	0.81[ASN][1000 genomes]
rs7430334	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs7613360	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613875	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7615206	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621026	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7626952	0.92[ASN][1000 genomes]
rs7627864	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627910	0.92[ASN][1000 genomes]
rs7628058	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7648174	0.83[ASN][1000 genomes]
rs868891	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9311446	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs952594	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814664	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9843653	0.82[ASN][1000 genomes]
rs9861216	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9862795	0.82[ASN][1000 genomes]
rs9866695	0.90[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs11712056	RNF123	cis	parietal	SCAN
rs11712056	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11712056	RBM6	cis	Artery Tibial	GTEx
rs11712056	RBM6	cis	Heart Left Ventricle	GTEx
rs11712056	RBM6	cis	cerebellum	SCAN
rs11712056	CELSR3	cis	parietal	SCAN
rs11712056	RBM6	cis	parietal	SCAN
rs11712056	RBM6	cis	Adipose Subcutaneous	GTEx
rs11712056	RBM6	cis	Thyroid	GTEx
rs11712056	RBM6	cis	Whole Blood	GTEx
rs11712056	RBM6	cis	Artery Aorta	GTEx
rs11712056	RNF123	cis	cerebellum	SCAN
rs11712056	RBM6	cis	lymphoblastoid	seeQTL
rs11712056	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs11712056	RBM6	cis	lung	GTEx
rs11712056	RBM6	cis	Esophagus Muscularis	GTEx
rs11712056	RBM6	cis	Nerve Tibial	GTEx
rs11712056	QRICH1	cis	cerebellum	SCAN
rs11712056	ARIH2	cis	cerebellum	SCAN
rs11712056	RBM6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49910000-49917200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49910600-49914800	Weak transcription	Fetal Lung	lung
3	chr3:49910600-49916200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:49911000-49917200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:49911200-49914600	Weak transcription	Fetal Brain Female	brain
6	chr3:49911200-49917200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:49911800-49918600	Weak transcription	Colonic Mucosa	Colon
8	chr3:49912000-49919000	Weak transcription	Spleen	Spleen
9	chr3:49912200-49914600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:49912400-49917800	Weak transcription	Stomach Mucosa	stomach
11	chr3:49912800-49914800	Weak transcription	Fetal Intestine Small	intestine
12	chr3:49913600-49915000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:49913800-49914400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:49914200-49917800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49914200-49918800	Enhancers	Fetal Brain Male	brain

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