Variant report

Variant	rs3733134
Chromosome Location	chr3:49939503-49939504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr3:49939483-49939514	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:49939501-49941825	HCT-116	colon:	n/a	n/a
3	YY1	chr3:49939389-49939728	GM12878	blood:	n/a	n/a
4	YY1	chr3:49939414-49939701	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:49939484-49941805	Hela-S3	cervix:	n/a	n/a
6	RELA	chr3:49939325-49939805	GM12891	blood:	n/a	n/a
7	YY1	chr3:49939386-49939673	GM12878	blood:	n/a	n/a
8	YY1	chr3:49939396-49939753	GM12892	blood:	n/a	n/a
9	YY1	chr3:49939393-49939673	GM12891	blood:	n/a	n/a
10	TBP	chr3:49939424-49939655	Hela-S3	cervix:	n/a	n/a
11	RELA	chr3:49939358-49939680	GM18505	blood:	n/a	n/a
12	TBL1XR1	chr3:49939461-49939713	GM12878	blood:	n/a	n/a
13	RUNX3	chr3:49939360-49939626	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49939339-49939767	GM12892	blood:	n/a	n/a
15	RUNX3	chr3:49939328-49939789	GM12878	blood:	n/a	n/a
16	CEBPB	chr3:49939378-49939621	Hela-S3	cervix:	n/a	n/a
17	PBX3	chr3:49939427-49939609	GM12878	blood:	n/a	n/a
18	EBF1	chr3:49939404-49939672	GM12878	blood:	n/a	n/a
19	RELA	chr3:49939371-49939746	GM19099	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49907025..49909566-chr3:49939184..49940917,2	K562	blood:
2	chr3:49839049..49842350-chr3:49936029..49940414,4	K562	blood:
3	chr3:49937512..49940184-chr3:49951912..49954370,2	MCF-7	breast:
4	chr3:49844713..49846618-chr3:49938018..49940554,2	K562	blood:
5	chr3:49927718..49929244-chr3:49938416..49939964,2	MCF-7	breast:
6	chr3:49838036..49840305-chr3:49938057..49940452,2	MCF-7	breast:
7	chr3:49932972..49936126-chr3:49936946..49940007,3	MCF-7	breast:
8	chr3:49936090..49937594-chr3:49939320..49940938,2	K562	blood:
9	chr3:49837665..49841605-chr3:49939148..49941365,3	K562	blood:
10	chr3:49933351..49938041-chr3:49938966..49942332,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228008	TF binding region
ENSG00000185614	Chromatin interaction
ENSG00000230698	Chromatin interaction
ENSG00000164076	Chromatin interaction
ENSG00000164078	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11130222	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130224	0.82[AMR][1000 genomes]
rs11706185	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11709503	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11709573	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712056	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713193	0.82[AMR][1000 genomes]
rs11714324	0.95[ASN][1000 genomes]
rs11721204	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634780	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13077403	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13079006	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13082703	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17657664	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17657688	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352969	0.95[ASN][1000 genomes]
rs2352984	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526747	0.80[ASN][1000 genomes]
rs2526750	0.82[AMR][1000 genomes]
rs2624815	0.80[ASN][1000 genomes]
rs2624819	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624821	0.91[ASN][1000 genomes]
rs2624832	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681776	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2681779	0.81[ASN][1000 genomes]
rs2883059	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34034116	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312088	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34654589	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35275715	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36022378	0.87[ASN][1000 genomes]
rs3774759	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796386	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688688	0.88[ASN][1000 genomes]
rs4688753	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4688754	0.80[ASN][1000 genomes]
rs55692411	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62262114	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6446194	0.80[AFR][1000 genomes]
rs6446195	0.80[ASN][1000 genomes]
rs6762477	0.80[ASN][1000 genomes]
rs6774354	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793528	0.80[ASN][1000 genomes]
rs6795703	0.82[AMR][1000 genomes]
rs7430334	0.80[ASN][1000 genomes]
rs7613360	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7615206	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626952	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7627864	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7627910	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634441	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7648174	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868891	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952594	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9682295	0.80[ASN][1000 genomes]
rs9843653	0.81[AMR][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	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
4	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3733134	RBM6	cis	Artery Aorta	GTEx
rs3733134	RBM6	cis	Esophagus Muscularis	GTEx
rs3733134	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs3733134	RBM6	cis	Thyroid	GTEx
rs3733134	RBM6	cis	Nerve Tibial	GTEx
rs3733134	RBM6	cis	Artery Tibial	GTEx
rs3733134	RBM6	cis	Heart Left Ventricle	GTEx
rs3733134	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs3733134	RBM6	cis	Esophagus Mucosa	GTEx
rs3733134	RBM6	cis	Adipose Subcutaneous	GTEx
rs3733134	RBM6	cis	Whole Blood	GTEx
rs3733134	RBM6	cis	lung	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
2	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:49927600-49940400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:49928600-49943000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:49929600-49941200	Weak transcription	Ovary	ovary
6	chr3:49931400-49943600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:49933400-49939600	Weak transcription	Fetal Brain Female	brain
8	chr3:49933800-49941400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:49934400-49941400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:49935400-49940000	Weak transcription	Spleen	Spleen
11	chr3:49936200-49941000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:49936400-49940800	Enhancers	Pancreas	Pancrea
13	chr3:49936800-49939600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:49937000-49940800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr3:49937400-49940200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:49937600-49940800	Enhancers	K562	blood
17	chr3:49937600-49941000	Enhancers	Placenta	Placenta
18	chr3:49937600-49943200	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:49937800-49940400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:49938000-49939600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:49938000-49940000	Genic enhancers	Fetal Intestine Small	intestine
22	chr3:49938000-49941400	Enhancers	GM12878-XiMat	blood
23	chr3:49938200-49940600	Enhancers	Fetal Stomach	stomach
24	chr3:49938200-49940800	Enhancers	Fetal Muscle Leg	muscle
25	chr3:49938200-49941800	Flanking Active TSS	HMEC	breast
26	chr3:49938400-49940800	Enhancers	Colon Smooth Muscle	Colon
27	chr3:49938400-49941000	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:49938600-49940000	Enhancers	Fetal Lung	lung
29	chr3:49938600-49940000	Enhancers	Dnd41	blood
30	chr3:49938600-49941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:49938800-49939600	Active TSS	Colonic Mucosa	Colon
32	chr3:49938800-49939600	Active TSS	Duodenum Mucosa	Duodenum
33	chr3:49938800-49939800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:49938800-49940200	Weak transcription	Adipose Nuclei	Adipose
35	chr3:49938800-49940400	Weak transcription	Right Ventricle	heart
36	chr3:49938800-49940600	Enhancers	A549	lung
37	chr3:49938800-49940800	Weak transcription	Left Ventricle	heart
38	chr3:49938800-49941000	Weak transcription	Psoas Muscle	Psoas
39	chr3:49938800-49943200	Weak transcription	HSMMtube	muscle
40	chr3:49938800-49943200	Weak transcription	NH-A	brain
41	chr3:49939000-49939600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:49939000-49939600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:49939000-49940000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:49939000-49940000	Active TSS	Stomach Mucosa	stomach
45	chr3:49939000-49940400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:49939000-49941000	Weak transcription	Osteobl	bone
47	chr3:49939000-49941200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:49939000-49941200	Weak transcription	NHLF	lung
49	chr3:49939000-49941400	Active TSS	Hela-S3	cervix
50	chr3:49939000-49941600	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links