Variant report

Variant	rs6545027
Chromosome Location	chr2:48520670-48520671
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	chr2:48520183..48522872-chr2:48541558..48543622,2	MCF-7	breast:
2	chr2:48514433..48519005-chr2:48519179..48522844,4	K562	blood:

Variant related genes	Relation type
ENSG00000170802	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10153773	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10174717	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10180295	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10186237	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10193072	0.93[ASN][1000 genomes]
rs10199431	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs10208124	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10454133	0.84[CEU][hapmap]
rs10495951	0.82[JPT][hapmap]
rs10495952	0.82[JPT][hapmap]
rs11676168	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11679523	0.82[JPT][hapmap]
rs11680916	0.87[JPT][hapmap]
rs11682044	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11685861	0.88[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs11688481	0.82[JPT][hapmap]
rs11690690	0.83[JPT][hapmap];0.93[YRI][hapmap]
rs11690748	0.82[JPT][hapmap]
rs11690845	0.82[JPT][hapmap]
rs12616792	0.93[ASN][1000 genomes]
rs12713008	0.93[ASN][1000 genomes]
rs12713009	0.85[ASN][1000 genomes]
rs13383364	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13385535	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13386751	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13387171	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13388291	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13426834	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13432998	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17037289	0.82[JPT][hapmap]
rs17037298	0.82[JPT][hapmap]
rs17855177	0.82[JPT][hapmap]
rs2471405	0.91[ASN][1000 genomes]
rs28806843	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28841370	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4267555	0.81[CEU][hapmap]
rs4290706	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4344965	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4411759	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4547573	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4641990	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs56352447	0.88[ASN][1000 genomes]
rs57668696	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58660534	0.85[ASN][1000 genomes]
rs59264464	0.86[ASN][1000 genomes]
rs59412192	0.86[ASN][1000 genomes]
rs59761994	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60677957	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62136987	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137001	0.85[ASN][1000 genomes]
rs62137002	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137003	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137005	0.85[ASN][1000 genomes]
rs62137006	0.86[ASN][1000 genomes]
rs62137007	0.86[ASN][1000 genomes]
rs62137008	0.83[ASN][1000 genomes]
rs62137009	0.83[ASN][1000 genomes]
rs62138801	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545026	0.92[YRI][hapmap]
rs6545028	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545029	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545030	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545034	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545035	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545036	0.88[CEU][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs6705802	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs6712029	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6718068	0.82[JPT][hapmap]
rs6743757	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs6757206	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72818493	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820405	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72887649	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7340322	0.94[ASN][1000 genomes]
rs7562069	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs7562816	0.83[JPT][hapmap]
rs7566239	0.83[JPT][hapmap];0.96[YRI][hapmap]
rs7568960	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7576964	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs7577237	0.82[JPT][hapmap];0.96[YRI][hapmap]
rs7579932	0.85[CEU][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap]
rs7600794	0.89[CEU][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap]
rs7606104	0.88[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs9309152	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48506000-48539000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:48516800-48522200	Weak transcription	Primary B cells from peripheral blood	blood

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