Variant report

Variant	rs952594
Chromosome Location	chr3:49908023-49908024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1062633	0.81[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs11130222	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs11706185	0.82[AMR][1000 genomes]
rs11709573	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11712056	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]
rs11714324	0.93[ASN][1000 genomes]
rs11721204	0.83[AMR][1000 genomes];0.92[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];0.84[YRI][hapmap]
rs13060128	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs13077403	0.89[ASN][1000 genomes]
rs13079006	0.85[ASN][1000 genomes]
rs13082703	0.85[ASN][1000 genomes]
rs17657664	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs17657688	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs2230590	0.90[CHD][hapmap];0.82[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];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2352984	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2353579	0.82[JPT][hapmap]
rs2526747	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[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];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2624821	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2624822	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2624832	0.85[ASN][1000 genomes]
rs2624843	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2681776	0.85[ASN][1000 genomes]
rs2681779	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][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	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34034116	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34312088	0.85[ASN][1000 genomes]
rs34654589	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35275715	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36022378	0.95[ASN][1000 genomes]
rs3733134	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774759	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796386	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688688	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
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];0.82[YRI][hapmap]
rs4688755	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688758	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs55692411	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62262114	0.85[ASN][1000 genomes]
rs6446193	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6762477	0.87[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[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[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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];0.83[YRI][hapmap]
rs7430334	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs7613360	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621026	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7626952	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7627864	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627910	0.89[ASN][1000 genomes]
rs7628058	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7648174	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs868891	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311446	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9814664	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9861216	0.90[CHD][hapmap];0.82[JPT][hapmap]
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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs952594	RBM6	cis	lung	GTEx
rs952594	RBM6	cis	Whole Blood	GTEx
rs952594	RBM6	cis	Heart Left Ventricle	GTEx
rs952594	RBM6	cis	Artery Tibial	GTEx
rs952594	RBM6	cis	parietal	SCAN
rs952594	CELSR3	cis	parietal	SCAN
rs952594	RBM6	cis	lymphoblastoid	seeQTL
rs952594	RBM6	cis	Esophagus Mucosa	GTEx
rs952594	RBM6	cis	Adipose Subcutaneous	GTEx
rs952594	RNF123	cis	cerebellum	SCAN
rs952594	RNF123	cis	parietal	SCAN
rs952594	RBM6	cis	Nerve Tibial	GTEx
rs952594	RBM6	cis	Esophagus Muscularis	GTEx
rs952594	RBM6	cis	cerebellum	SCAN
rs952594	RBM6	cis	Thyroid	GTEx
rs952594	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs952594	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs952594	ARIH2	cis	cerebellum	SCAN
rs952594	QRICH1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49906200-49908200	Active TSS	Brain Anterior Caudate	brain
2	chr3:49906600-49910800	Enhancers	Fetal Brain Male	brain
3	chr3:49907400-49908200	Bivalent Enhancer	Brain Hippocampus Middle	brain
4	chr3:49907600-49908200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:49907600-49908600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:49907600-49909000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49907600-49909400	Enhancers	Brain Angular Gyrus	brain
8	chr3:49907600-49909400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:49907600-49910800	Weak transcription	Gastric	stomach
10	chr3:49907800-49908400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:49907800-49908600	Bivalent Enhancer	Fetal Intestine Small	intestine
12	chr3:49907800-49908800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:49907800-49909600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:49907800-49911000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49907800-49911200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:49908000-49909400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:49908000-49910000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:49908000-49911200	Enhancers	Fetal Brain Female	brain
19	chr3:49908000-49913600	Enhancers	Fetal Intestine Large	intestine

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