Variant report

Variant	rs34996346
Chromosome Location	chr4:26855549-26855550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26854192..26856257-chr4:26857515..26860025,3	MCF-7	breast:
2	chr4:26853806..26855714-chr4:26857731..26859878,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10029307	0.89[ASN][1000 genomes]
rs11729927	0.89[ASN][1000 genomes]
rs11730235	0.89[ASN][1000 genomes]
rs11734308	0.87[ASN][1000 genomes]
rs11737218	0.95[ASN][1000 genomes]
rs11943948	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12641261	0.96[ASN][1000 genomes]
rs12644073	0.91[ASN][1000 genomes]
rs12646473	0.95[ASN][1000 genomes]
rs12650172	0.96[ASN][1000 genomes]
rs13116341	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13138942	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13139464	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28497454	0.89[ASN][1000 genomes]
rs28520489	0.87[ASN][1000 genomes]
rs3792685	0.82[ASN][1000 genomes]
rs3924178	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4274829	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4407490	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4505809	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4519790	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4532223	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4557250	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4557251	0.98[ASN][1000 genomes]
rs57663175	0.88[ASN][1000 genomes]
rs57686546	0.88[ASN][1000 genomes]
rs58075729	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58968032	0.94[ASN][1000 genomes]
rs60890366	0.86[ASN][1000 genomes]
rs61047003	0.87[ASN][1000 genomes]
rs62302532	0.85[ASN][1000 genomes]
rs62302533	0.85[ASN][1000 genomes]
rs62302535	0.84[ASN][1000 genomes]
rs6448479	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6448484	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6448488	0.85[ASN][1000 genomes]
rs6815719	0.96[ASN][1000 genomes]
rs6833053	0.96[ASN][1000 genomes]
rs6833895	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6835631	0.86[ASN][1000 genomes]
rs6844153	0.86[ASN][1000 genomes]
rs6853032	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73116683	0.86[ASN][1000 genomes]
rs73811400	0.95[ASN][1000 genomes]
rs73813220	0.89[ASN][1000 genomes]
rs7655686	0.90[ASN][1000 genomes]
rs9790789	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[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	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	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
4	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs34996346	RP11-293A21.1	cis	Muscle Skeletal	GTEx
rs34996346	RP11-293A21.1	cis	Thyroid	GTEx
rs34996346	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs34996346	RP11-293A21.1	cis	Adipose Subcutaneous	GTEx
rs34996346	RP11-293A21.1	cis	lung	GTEx
rs34996346	RP11-293A21.1	cis	Esophagus Mucosa	GTEx
rs34996346	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 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	chr4:26841400-26858600	Weak transcription	Aorta	Aorta
3	chr4:26841600-26858600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:26842400-26858800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:26843400-26858400	Weak transcription	Thymus	Thymus
6	chr4:26850200-26858800	Weak transcription	HSMM	muscle
7	chr4:26851600-26858600	Weak transcription	Monocytes-CD14+_RO01746	blood

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