Variant report

Variant	rs4687545
Chromosome Location	chr3:52537969-52537970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:52537656-52538136	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:52537269-52538226	HUVEC	blood vessel:	n/a	n/a
3	TCF12	chr3:52537900-52538119	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr3:52537940-52538090	GM12865	blood:	n/a	chr3:52537963-52537976
5	CTCF	chr3:52537911-52537994	H1-hESC	embryonic stem cell:	n/a	chr3:52537963-52537976
6	RAD21	chr3:52537808-52537992	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr3:52537876-52538031	HepG2	liver:	n/a	n/a
8	CTCF	chr3:52537820-52537970	WERI-Rb-1	eye:	n/a	n/a
9	CTCF	chr3:52537860-52538010	HepG2	liver:	n/a	chr3:52537963-52537976
10	POLR2A	chr3:52537108-52538045	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:52536311-52538135	HUVEC	blood vessel:	n/a	n/a
12	SIN3A	chr3:52537921-52537970	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr3:52537902-52538255	ECC-1	luminal epithelium:	n/a	chr3:52537979-52537988 chr3:52537994-52538004

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52537920..52539549-chr3:52569370..52573115,4	K562	blood:
2	chr3:52504996..52506918-chr3:52535565..52538055,2	MCF-7	breast:
3	chr3:52537807..52540311-chr3:52607410..52609955,2	MCF-7	breast:
4	chr3:52535112..52538485-chr3:52564476..52567424,4	K562	blood:
5	chr3:52532062..52534916-chr3:52535199..52537993,2	K562	blood:
6	chr3:52537241..52538905-chr3:52567545..52569543,2	K562	blood:
7	chr3:52534136..52536462-chr3:52536613..52538164,2	MCF-7	breast:
8	chr3:52536407..52539525-chr3:52571038..52574825,3	K562	blood:

No data

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1011062	1.00[AFR][1000 genomes]
rs11709658	1.00[JPT][hapmap]
rs11721286	1.00[AFR][1000 genomes]
rs13066389	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066644	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086936	1.00[CEU][hapmap]
rs13099479	0.90[CEU][hapmap]
rs13326165	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2109559	1.00[AFR][1000 genomes]
rs2335929	1.00[AFR][1000 genomes]
rs34735556	0.82[ASN][1000 genomes]
rs35225119	0.82[ASN][1000 genomes]
rs35272104	0.82[ASN][1000 genomes]
rs35325270	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35371456	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35911561	0.90[CEU][hapmap]
rs3733043	1.00[JPT][hapmap]
rs3774409	1.00[AFR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs4312651	1.00[AFR][1000 genomes]
rs4687541	1.00[AFR][1000 genomes]
rs4687543	1.00[AFR][1000 genomes]
rs4687617	1.00[AFR][1000 genomes]
rs4687618	1.00[AFR][1000 genomes]
rs4687619	1.00[AFR][1000 genomes]
rs4687621	1.00[AFR][1000 genomes]
rs6414568	1.00[AFR][1000 genomes]
rs6445486	1.00[AFR][1000 genomes]
rs6445506	1.00[AFR][1000 genomes]
rs6771558	1.00[AFR][1000 genomes]
rs67749743	1.00[ASN][1000 genomes]
rs6782162	1.00[AFR][1000 genomes]
rs6810027	1.00[AFR][1000 genomes]
rs728408	1.00[AFR][1000 genomes]
rs758801	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs758802	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758803	1.00[AFR][1000 genomes]
rs7614424	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[AFR][1000 genomes]
rs7644763	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846089	1.00[AFR][1000 genomes]
rs9850471	1.00[AFR][1000 genomes]
rs9855470	1.00[AFR][1000 genomes]
rs9863753	1.00[AFR][1000 genomes]
rs9867823	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS 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	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4687545	GNL3	cis	Skin Sun Exposed Lower leg	GTEx
rs4687545	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52513400-52541400	Weak transcription	A549	lung
2	chr3:52527000-52538000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:52527000-52540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52530000-52538800	Weak transcription	Gastric	stomach
5	chr3:52530200-52551800	Weak transcription	Esophagus	oesophagus
6	chr3:52530400-52552400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:52530800-52548200	Weak transcription	Right Ventricle	heart
9	chr3:52530800-52551600	Weak transcription	Fetal Intestine Small	intestine
10	chr3:52531000-52547600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:52533400-52540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:52533400-52549200	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:52533400-52549200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:52533400-52559800	Weak transcription	Liver	Liver
16	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:52535200-52538600	Weak transcription	Placenta	Placenta
18	chr3:52535400-52538800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:52535400-52539800	Strong transcription	HUVEC	blood vessel
20	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:52535600-52541600	Strong transcription	Lung	lung
22	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:52536400-52538600	Enhancers	Fetal Muscle Trunk	muscle
24	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:52536800-52539000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:52536800-52542000	Weak transcription	Fetal Stomach	stomach
27	chr3:52536800-52552600	Strong transcription	Adipose Nuclei	Adipose
28	chr3:52537000-52539000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:52537400-52539600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:52537400-52541000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
31	chr3:52537600-52538800	Enhancers	Pancreas	Pancrea
32	chr3:52537600-52539000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:52537800-52538400	Strong transcription	Spleen	Spleen

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