Variant report

Variant	rs4519790
Chromosome Location	chr4:26844674-26844675
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:26843830..26846151-chr4:26857886..26860220,2	MCF-7	breast:
2	chr4:26837478..26839515-chr4:26843202..26845987,2	MCF-7	breast:
3	chr4:26842658..26844701-chr4:26856805..26859356,2	K562	blood:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029307	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11729927	0.87[ASN][1000 genomes]
rs11730235	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11734308	0.85[ASN][1000 genomes]
rs11737218	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11943948	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12641261	0.94[ASN][1000 genomes]
rs12644073	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12646473	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs12650172	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13116341	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13138942	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13139464	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28497454	0.87[ASN][1000 genomes]
rs28520489	0.86[ASN][1000 genomes]
rs34996346	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792685	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3924178	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4274829	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4407490	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4505809	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4532223	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4557250	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4557251	0.96[ASN][1000 genomes]
rs57663175	0.87[ASN][1000 genomes]
rs57686546	0.86[ASN][1000 genomes]
rs58075729	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58968032	0.92[ASN][1000 genomes]
rs60890366	0.85[ASN][1000 genomes]
rs61047003	0.85[ASN][1000 genomes]
rs62302532	0.84[ASN][1000 genomes]
rs62302533	0.84[ASN][1000 genomes]
rs62302535	0.82[ASN][1000 genomes]
rs6448479	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448484	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6448488	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6815719	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6833053	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6833895	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6835631	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6844153	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6853032	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73116683	0.84[ASN][1000 genomes]
rs73811400	0.94[ASN][1000 genomes]
rs73813220	0.88[ASN][1000 genomes]
rs7655686	0.89[ASN][1000 genomes]
rs9790789	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv521924	chr4:26843494-26844674	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4519790	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs4519790	RP11-293A21.1	cis	Adipose Subcutaneous	GTEx
rs4519790	STIM2	cis	multi-tissue	Pritchard
rs4519790	RP11-293A21.1	cis	Thyroid	GTEx
rs4519790	RP11-293A21.1	cis	Muscle Skeletal	GTEx
rs4519790	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4519790	STIM2	cis	lymphoblastoid	seeQTL
rs4519790	RP11-293A21.1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26840000-26858800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:26841400-26845400	Weak transcription	Gastric	stomach
3	chr4:26841400-26858600	Weak transcription	Aorta	Aorta
4	chr4:26841600-26858600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:26842400-26858800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:26842800-26845800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:26842800-26846400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:26843400-26858400	Weak transcription	Thymus	Thymus
9	chr4:26844200-26845200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:26844200-26845200	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr4:26844400-26845000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr4:26844400-26845000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:26844600-26845000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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