Variant report

Variant	rs2777888
Chromosome Location	chr3:49898000-49898001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49893970..49895819-chr3:49897460..49901140,3	K562	blood:
2	chr3:49893997..49896267-chr3:49897540..49900036,2	MCF-7	breast:
3	chr3:49897011..49898757-chr3:49905892..49907446,2	K562	blood:
4	chr3:49897257..49899653-chr3:49900081..49902662,3	K562	blood:
5	chr3:49896228..49898642-chr3:49905668..49907907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264706	Chromatin interaction
ENSG00000164076	Chromatin interaction
ENSG00000183763	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1049256	0.80[CEU][hapmap]
rs1062633	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130218	0.80[CEU][hapmap]
rs11130219	0.80[CEU][hapmap]
rs11130224	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130233	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11709573	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs11709680	0.80[CEU][hapmap]
rs11712056	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs11713193	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11716575	0.80[CEU][hapmap]
rs12496973	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs12634780	0.82[JPT][hapmap]
rs13060128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs1317154	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1491986	0.84[CEU][hapmap]
rs17657664	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs17657688	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2230590	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2234391	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs2245365	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2246832	0.83[CHB][hapmap]
rs2252833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs2271960	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs2271961	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs2280406	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2352969	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2352974	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs2352984	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2353579	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2526747	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2526748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs2526751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2624819	0.82[JPT][hapmap]
rs2624821	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2624824	0.92[CEU][hapmap]
rs2624843	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs2681779	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2681780	0.94[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[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2681781	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2883057	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2883059	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs35261599	0.80[CEU][hapmap]
rs3733135	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3749240	0.80[CEU][hapmap]
rs3774733	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774758	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3774759	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs3796386	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs4688690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs4688753	0.82[JPT][hapmap]
rs4688755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs4688758	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs4855862	0.80[CEU][hapmap]
rs4855867	0.80[CEU][hapmap]
rs55751738	0.82[AMR][1000 genomes]
rs62262093	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6446187	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6446189	0.81[AMR][1000 genomes]
rs6446193	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs6762477	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6765484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs6771546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes]
rs6772095	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs6774354	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6775384	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs6785549	0.80[CEU][hapmap]
rs6792892	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs6795703	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6802890	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs695238	0.80[CEU][hapmap];0.92[CHB][hapmap]
rs72942333	0.81[AMR][1000 genomes]
rs7372966	0.80[CEU][hapmap]
rs7374183	0.80[CEU][hapmap]
rs7430334	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7609971	0.83[AMR][1000 genomes]
rs7613875	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs7615206	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7621026	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes]
rs7621352	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7627864	0.82[JPT][hapmap]
rs7628058	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7634084	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7634902	0.80[CEU][hapmap]
rs7635002	0.81[AMR][1000 genomes]
rs7645061	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs7648987	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs7649348	0.80[CEU][hapmap]
rs868891	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9311446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs952594	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9814664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs9815766	0.80[CEU][hapmap]
rs9821675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9843653	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9848497	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9853222	0.81[AMR][1000 genomes]
rs9855505	0.80[CEU][hapmap]
rs9859153	0.80[CEU][hapmap]
rs9861216	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs9862795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9866695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs9872864	0.80[CEU][hapmap]
rs9876508	0.80[CEU][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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs2777888	RBM6	cis	Artery Aorta	GTEx
rs2777888	RBM6	cis	lung	GTEx
rs2777888	RNF123	cis	parietal	SCAN
rs2777888	ACTBP13	cis	Skin Sun Exposed Lower leg	GTEx
rs2777888	RBM6	cis	cerebellum	SCAN
rs2777888	RNF123	cis	cerebellum	SCAN
rs2777888	ARIH2	cis	cerebellum	SCAN
rs2777888	RBM6	cis	temporal cortex	BrainEAC
rs2777888	RBM6	cis	Adipose Subcutaneous	GTEx
rs2777888	RBM6	cis	lymphoblastoid	seeQTL
rs2777888	RBM6	cis	Nerve Tibial	GTEx
rs2777888	RBM6	cis	Heart Left Ventricle	GTEx
rs2777888	RBM6	cis	Stomach	GTEx
rs2777888	C3orf54	cis	cerebellum	SCAN
rs2777888	RBM6	cis	Esophagus Mucosa	GTEx
rs2777888	RBM6	cis	Whole Blood	GTEx
rs2777888	RBM6	cis	brain	BrainEAC
rs2777888	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2777888	RBM6	cis	parietal	SCAN
rs2777888	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2777888	CYB561D2	cis	cerebellum	SCAN
rs2777888	RBM6	cis	Artery Tibial	GTEx
rs2777888	RBM6	cis	Thyroid	GTEx
rs2777888	RBM6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49894600-49899200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:49894600-49899400	Weak transcription	Brain Angular Gyrus	brain
3	chr3:49894600-49902000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:49894600-49903000	Weak transcription	Gastric	stomach
5	chr3:49894600-49903600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:49894600-49903800	Weak transcription	Fetal Intestine Large	intestine
7	chr3:49894600-49904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49894600-49906400	Weak transcription	Right Atrium	heart
9	chr3:49894800-49900000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:49894800-49901000	Weak transcription	Fetal Brain Male	brain
11	chr3:49895200-49899400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49895200-49899600	Strong transcription	Fetal Brain Female	brain
13	chr3:49895200-49900000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:49895400-49899000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:49895600-49899000	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr3:49896200-49898400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:49896200-49899400	Strong transcription	Brain Germinal Matrix	brain
18	chr3:49896200-49899800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:49896400-49899400	Strong transcription	Brain Anterior Caudate	brain
20	chr3:49896400-49899800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:49896400-49899800	Strong transcription	Fetal Intestine Small	intestine
22	chr3:49896400-49900000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:49896800-49898400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:49896800-49899000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:49896800-49899000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:49896800-49899800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr3:49897000-49902800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:49897200-49899600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:49897400-49898800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:49897800-49898000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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