Variant report

Variant	rs13114545
Chromosome Location	chr4:26845759-26845760
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	chr4:26766814..26768633-chr4:26844844..26846857,2	MCF-7	breast:
3	chr4:26837478..26839515-chr4:26843202..26845987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10014701	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10022599	0.82[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs10030655	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs10213674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10470823	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]
rs10939141	0.86[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1122045	0.81[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs11722221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11722323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11730493	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13106956	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13127603	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]
rs28600019	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34506340	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4692127	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7655631	0.81[CEU][hapmap]
rs7660174	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7680110	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7688120	0.82[ASN][1000 genomes]
rs7688454	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7688662	0.82[ASW][hapmap];0.91[CEU][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13114545	STIM2	cis	multi-tissue	Pritchard
rs13114545	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs13114545	C4orf52	cis	parietal	SCAN

Chromatin state (count:8 , 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	chr4:26842800-26845800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:26842800-26846400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:26843400-26858400	Weak transcription	Thymus	Thymus
8	chr4:26845200-26850600	Weak transcription	Primary monocytes fromperipheralblood	blood

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