Variant report

Variant	rs7613360
Chromosome Location	chr3:49916710-49916711
allele	C/T
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	chr3:49916166-49923391	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:49911230-49922975	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49839311..49841661-chr3:49914034..49916864,2	K562	blood:
2	chr3:49908054..49910878-chr3:49916403..49919498,3	K562	blood:
3	chr3:49909687..49911283-chr3:49915526..49917285,2	K562	blood:

Variant related genes	Relation type
ACTBP13	TF binding region
ENSG00000185614	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1062633	0.81[ASN][1000 genomes]
rs11130222	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11709503	0.86[AFR][1000 genomes]
rs11709573	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712056	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713193	0.81[ASN][1000 genomes]
rs11714324	0.90[ASN][1000 genomes]
rs11721204	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13077403	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13079006	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13082703	0.83[ASN][1000 genomes]
rs17657664	0.83[ASN][1000 genomes]
rs17657688	0.83[ASN][1000 genomes]
rs2352969	0.84[ASN][1000 genomes]
rs2352984	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2624819	0.80[AMR][1000 genomes]
rs2624821	0.81[ASN][1000 genomes]
rs2624832	0.83[ASN][1000 genomes]
rs2681776	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2883059	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34034116	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34312088	0.83[ASN][1000 genomes]
rs34654589	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35275715	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36022378	0.98[ASN][1000 genomes]
rs3733134	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774759	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796386	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55692411	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62262114	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6774354	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795703	0.81[ASN][1000 genomes]
rs7615206	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7626952	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7627864	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627910	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7648174	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs868891	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs952594	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843653	0.82[ASN][1000 genomes]
rs9862795	0.82[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7613360	RBM6	cis	Esophagus Mucosa	GTEx
rs7613360	RBM6	cis	lung	GTEx
rs7613360	RBM6	cis	Nerve Tibial	GTEx
rs7613360	RBM6	cis	Adipose Subcutaneous	GTEx
rs7613360	RBM6	cis	Esophagus Muscularis	GTEx
rs7613360	RBM6	cis	Artery Aorta	GTEx
rs7613360	RBM6	cis	Artery Tibial	GTEx
rs7613360	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs7613360	RBM6	cis	Whole Blood	GTEx
rs7613360	RBM6	cis	Thyroid	GTEx

Chromatin state (count:20 , 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	chr3:49911000-49917200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:49911200-49917200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:49911800-49918600	Weak transcription	Colonic Mucosa	Colon
5	chr3:49912000-49919000	Weak transcription	Spleen	Spleen
6	chr3:49912400-49917800	Weak transcription	Stomach Mucosa	stomach
7	chr3:49914200-49917800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49914200-49918800	Enhancers	Fetal Brain Male	brain
9	chr3:49914600-49917200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:49914600-49918000	Enhancers	Fetal Brain Female	brain
11	chr3:49914600-49920200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:49915200-49917000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:49915400-49917200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:49915600-49918000	Weak transcription	Fetal Stomach	stomach
15	chr3:49915600-49918600	Enhancers	HepG2	liver
16	chr3:49915800-49917200	Weak transcription	Fetal Lung	lung
17	chr3:49915800-49917800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:49916200-49917800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:49916400-49917200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:49916400-49917200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links