Variant report

Variant	rs4671968
Chromosome Location	chr2:54912259-54912260
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54907957..54910043-chr2:54910399..54913105,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1027950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1052788	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1052820	0.91[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12475342	0.89[JPT][hapmap]
rs12611806	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12612665	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12620195	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12622340	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1510612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17046153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17416284	0.91[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1848923	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2007020	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2567837	0.87[ASN][1000 genomes]
rs354188	0.93[ASN][1000 genomes]
rs354215	0.93[ASN][1000 genomes]
rs3817163	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs4519565	0.80[CEU][hapmap]
rs4671224	0.80[CEU][hapmap]
rs4671229	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4671952	0.84[CEU][hapmap]
rs4671959	0.83[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4671962	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4671965	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs4671966	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56898160	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545433	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6545438	0.91[CHB][hapmap]
rs6705756	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6738725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72618665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72618666	0.87[EUR][1000 genomes]
rs72618667	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72618668	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72618669	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9309255	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4671968	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL
rs4671968	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54903400-54915600	Weak transcription	Right Atrium	heart
2	chr2:54908000-54914800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:54908200-54914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:54908800-54921400	Weak transcription	Lung	lung
5	chr2:54911000-54918600	Weak transcription	HepG2	liver
6	chr2:54911000-54919000	Weak transcription	Pancreas	Pancrea
7	chr2:54911200-54914800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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