Variant report

Variant	rs4254702
Chromosome Location	chr3:160174138-160174139
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160169346..160171536-chr3:160172001..160174189,2	MCF-7	breast:
2	chr3:160172072..160175654-chr3:160182071..160184575,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244009	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10936199	0.82[CEU][hapmap]
rs1141023	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236389	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236452	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236487	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs17826161	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882124	0.84[ASN][1000 genomes]
rs1882128	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1920645	1.00[JPT][hapmap]
rs1920648	0.84[ASN][1000 genomes]
rs1920654	0.84[ASN][1000 genomes]
rs1979160	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2029361	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2152424	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2272489	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35281166	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3737214	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41272955	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434183	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679879	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs4679880	0.83[CEU][hapmap]
rs4679883	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679887	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679894	0.88[CEU][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4680577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680590	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55853078	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930449	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56030166	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56051094	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322040	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776582	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6778728	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs6780828	0.84[ASN][1000 genomes]
rs6806971	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154549	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154552	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154567	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154591	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154596	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154600	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154602	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155903	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155920	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155922	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155924	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7622031	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826290	0.92[ASN][1000 genomes]
rs9845172	0.84[ASN][1000 genomes]
rs9847144	0.84[ASN][1000 genomes]
rs9876980	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS 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 miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160170200-160175600	Weak transcription	K562	blood
2	chr3:160173200-160174600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:160173200-160174800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:160173200-160174800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:160173400-160175400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:160173800-160175000	Enhancers	Brain Angular Gyrus	brain

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