Variant report

Variant	rs2164553
Chromosome Location	chr3:143688310-143688311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143687536..143689056-chr3:143689809..143691733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1125704	0.81[EUR][1000 genomes]
rs1125705	0.83[EUR][1000 genomes]
rs11710441	0.81[EUR][1000 genomes]
rs13083596	0.81[EUR][1000 genomes]
rs13092757	0.81[EUR][1000 genomes]
rs13323371	0.82[EUR][1000 genomes]
rs1370029	0.81[EUR][1000 genomes]
rs1370030	0.81[EUR][1000 genomes]
rs1394399	0.81[EUR][1000 genomes]
rs1394400	0.81[EUR][1000 genomes]
rs1394401	0.81[EUR][1000 genomes]
rs1504601	0.81[EUR][1000 genomes]
rs1583550	0.81[EUR][1000 genomes]
rs1595210	0.81[EUR][1000 genomes]
rs1595211	0.81[EUR][1000 genomes]
rs17603166	0.82[EUR][1000 genomes]
rs1898263	0.81[EUR][1000 genomes]
rs1992094	0.83[EUR][1000 genomes]
rs2118071	0.83[EUR][1000 genomes]
rs2118072	0.83[EUR][1000 genomes]
rs2134914	0.83[EUR][1000 genomes]
rs2134915	0.83[EUR][1000 genomes]
rs2134916	0.83[EUR][1000 genomes]
rs2164551	0.82[EUR][1000 genomes]
rs2164552	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2202378	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2217926	0.81[EUR][1000 genomes]
rs2221411	0.83[EUR][1000 genomes]
rs2887666	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35291263	0.81[EUR][1000 genomes]
rs4258964	0.82[EUR][1000 genomes]
rs4258965	0.83[EUR][1000 genomes]
rs4276180	0.84[EUR][1000 genomes]
rs4431106	0.82[EUR][1000 genomes]
rs4462961	0.82[EUR][1000 genomes]
rs4476500	0.83[EUR][1000 genomes]
rs4549268	0.83[EUR][1000 genomes]
rs4563410	0.83[EUR][1000 genomes]
rs4575896	0.83[EUR][1000 genomes]
rs4582058	0.84[EUR][1000 genomes]
rs6440207	0.81[EUR][1000 genomes]
rs6440208	0.81[EUR][1000 genomes]
rs6440209	0.81[EUR][1000 genomes]
rs67417607	0.81[EUR][1000 genomes]
rs723490	0.83[EUR][1000 genomes]
rs723492	0.83[EUR][1000 genomes]
rs7432451	0.82[EUR][1000 genomes]
rs7611555	0.83[EUR][1000 genomes]
rs7611648	0.83[EUR][1000 genomes]
rs7619036	0.83[EUR][1000 genomes]
rs7619220	0.83[EUR][1000 genomes]
rs7622357	0.83[EUR][1000 genomes]
rs7626898	0.81[EUR][1000 genomes]
rs7628282	0.81[EUR][1000 genomes]
rs7631704	0.82[EUR][1000 genomes]
rs7638577	0.81[EUR][1000 genomes]
rs7643800	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7650233	0.80[EUR][1000 genomes]
rs7650239	0.80[EUR][1000 genomes]
rs7650332	0.81[EUR][1000 genomes]
rs7653287	0.83[EUR][1000 genomes]
rs7653431	0.82[EUR][1000 genomes]
rs9289671	0.83[EUR][1000 genomes]
rs9811736	0.81[EUR][1000 genomes]
rs9811888	0.81[EUR][1000 genomes]
rs9812340	0.82[EUR][1000 genomes]
rs9812374	0.81[EUR][1000 genomes]
rs9829883	0.81[EUR][1000 genomes]
rs9840157	0.81[EUR][1000 genomes]
rs9840971	0.81[EUR][1000 genomes]
rs9841182	0.80[EUR][1000 genomes]
rs9854844	0.81[EUR][1000 genomes]
rs9860872	0.80[EUR][1000 genomes]
rs9865128	0.80[EUR][1000 genomes]
rs9867025	0.81[EUR][1000 genomes]
rs9867615	0.81[EUR][1000 genomes]
rs9867976	0.81[EUR][1000 genomes]
rs9869178	0.82[EUR][1000 genomes]
rs9872448	0.81[EUR][1000 genomes]
rs9872595	0.81[EUR][1000 genomes]
rs9876654	0.81[EUR][1000 genomes]
rs9878070	0.81[EUR][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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3349108	chr3:143676303-143692796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143680400-143689600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:143682800-143688800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:143683400-143689200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:143683800-143689400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:143684000-143689600	Weak transcription	Pancreas	Pancrea
6	chr3:143685200-143689600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:143685600-143688800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:143685600-143689000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:143687600-143689400	Weak transcription	Right Atrium	heart
10	chr3:143688000-143689600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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