Variant report

Variant	rs34654589
Chromosome Location	chr3:49911449-49911450
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49910856-49911670	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:49911442-49911722	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:49911230-49922975	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:49911378-49912167	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49900314..49905841-chr3:49909576..49913570,6	K562	blood:
2	chr3:49910943..49912863-chr3:49914615..49917356,2	K562	blood:
3	chr3:49906989..49909987-chr3:49910807..49914298,3	K562	blood:

Variant related genes	Relation type
CAMKV	TF binding region
ENSG00000164076	Chromatin interaction
ENSG00000264706	Chromatin interaction
ENSG00000234667	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11130222	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11709573	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11712056	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11714324	0.93[ASN][1000 genomes]
rs11721204	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13077403	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13079006	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13082703	0.85[ASN][1000 genomes]
rs17657664	0.85[ASN][1000 genomes]
rs17657688	0.85[ASN][1000 genomes]
rs2352969	0.87[ASN][1000 genomes]
rs2352984	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624819	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2624821	0.84[ASN][1000 genomes]
rs2624832	0.85[ASN][1000 genomes]
rs2681776	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2883059	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34034116	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34312088	0.85[ASN][1000 genomes]
rs35275715	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36022378	0.95[ASN][1000 genomes]
rs3733134	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774759	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796386	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688688	0.81[ASN][1000 genomes]
rs55692411	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62262114	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6774354	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613360	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7615206	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7626952	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7627864	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627910	0.89[ASN][1000 genomes]
rs7648174	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs868891	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs952594	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs34654589	RBM6	cis	Nerve Tibial	GTEx
rs34654589	RBM6	cis	Esophagus Muscularis	GTEx
rs34654589	RBM6	cis	lung	GTEx
rs34654589	RBM6	cis	Esophagus Mucosa	GTEx
rs34654589	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs34654589	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs34654589	RBM6	cis	Artery Aorta	GTEx
rs34654589	RBM6	cis	Adipose Subcutaneous	GTEx
rs34654589	RBM6	cis	Artery Tibial	GTEx
rs34654589	RBM6	cis	Thyroid	GTEx
rs34654589	RBM6	cis	Heart Left Ventricle	GTEx
rs34654589	RBM6	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49908000-49913600	Enhancers	Fetal Intestine Large	intestine
2	chr3:49908200-49911600	Enhancers	Brain Anterior Caudate	brain
3	chr3:49910000-49912400	Enhancers	Stomach Mucosa	stomach
4	chr3:49910000-49917200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49910200-49911600	Enhancers	Small Intestine	intestine
6	chr3:49910200-49911800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:49910200-49912000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr3:49910400-49911600	Enhancers	Duodenum Mucosa	Duodenum
9	chr3:49910400-49911800	Enhancers	Colonic Mucosa	Colon
10	chr3:49910400-49911800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr3:49910600-49914800	Weak transcription	Fetal Lung	lung
12	chr3:49910600-49916200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:49910800-49911600	Enhancers	Gastric	stomach
14	chr3:49910800-49914200	Weak transcription	Fetal Brain Male	brain
15	chr3:49911000-49914200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49911000-49917200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:49911200-49914600	Weak transcription	Fetal Brain Female	brain
18	chr3:49911200-49917200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:49911400-49911600	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr3:49911400-49912000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:49911400-49912400	Genic enhancers	Fetal Intestine Small	intestine

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