Variant report

Variant	rs7609971
Chromosome Location	chr3:49975654-49975655
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	chr3:49965505..49970003-chr3:49974970..49980028,17	K562	blood:
2	chr3:49965568..49971141-chr3:49975411..49979217,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164077	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1062633	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11130224	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130226	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130228	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130229	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130233	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130234	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11713193	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11713562	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11925192	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12485600	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496973	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13060128	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1317154	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2230590	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252833	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280406	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2353579	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353586	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2353587	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526751	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2624843	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2624844	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2681778	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681780	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2681781	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2777888	0.83[AMR][1000 genomes]
rs2883057	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34080578	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35065728	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733135	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3774733	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774758	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688689	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688690	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688755	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4688756	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688757	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688758	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55751738	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62262093	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446187	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6446189	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446190	0.82[EUR][1000 genomes]
rs6446193	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6765484	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6767381	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771546	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6772095	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780731	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792892	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6795703	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72942333	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7613875	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621026	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621352	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7628058	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634084	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634917	0.83[EUR][1000 genomes]
rs7635002	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7650214	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9814664	0.80[EUR][1000 genomes]
rs9821433	0.84[ASN][1000 genomes]
rs9821675	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9843653	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9848497	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9853222	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861216	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862795	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9866695	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9881008	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv965334	chr3:49967342-50000012	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
5	nsv513047	chr3:49974660-49977265	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	esv2517369	chr3:49975235-49977296	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7609971	RBM6	cis	Thyroid	GTEx
rs7609971	RBM6	cis	Adipose Subcutaneous	GTEx
rs7609971	RBM6	cis	Esophagus Mucosa	GTEx
rs7609971	RBM6	cis	Heart Left Ventricle	GTEx
rs7609971	RBM6	cis	Artery Tibial	GTEx
rs7609971	RBM6	cis	Whole Blood	GTEx
rs7609971	RBM6	cis	Esophagus Muscularis	GTEx
rs7609971	RBM6	cis	Artery Aorta	GTEx
rs7609971	RBM6	cis	Nerve Tibial	GTEx
rs7609971	RBM6	cis	lung	GTEx
rs7609971	RBM6	cis	Stomach	GTEx
rs7609971	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs7609971	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49967600-49977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49967800-49977000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:49967800-49977000	Weak transcription	NHLF	lung
4	chr3:49968000-49976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:49968800-49976800	Weak transcription	HepG2	liver
6	chr3:49969200-49977000	Weak transcription	K562	blood
7	chr3:49973600-49976200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:49974600-49977000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:49974800-49976800	Weak transcription	GM12878-XiMat	blood
10	chr3:49975000-49976800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:49975000-49977000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr3:49975000-49977400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:49975200-49977000	Weak transcription	Adipose Nuclei	Adipose
14	chr3:49975400-49977000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:49975400-49977000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:49975600-49977000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:49975600-49977000	Weak transcription	Monocytes-CD14+_RO01746	blood

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