Variant report

Variant	rs12027539
Chromosome Location	chr1:224063971-224063972
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224033263..224035344-chr1:224063361..224065777,2	MCF-7	breast:
2	chr1:224032494..224036254-chr1:224057433..224064259,8	K562	blood:
3	chr1:224063820..224066455-chr1:224070379..224072043,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10158345	0.85[CHB][hapmap]
rs10799327	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs10915882	0.95[EUR][1000 genomes]
rs10915892	0.95[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs10915917	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915946	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915948	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915950	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915956	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1124943	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11801971	0.95[EUR][1000 genomes]
rs11802505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806886	0.89[EUR][1000 genomes]
rs12021759	0.99[EUR][1000 genomes]
rs12021785	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12024535	0.98[EUR][1000 genomes]
rs12026098	0.98[EUR][1000 genomes]
rs12026835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12030094	0.93[EUR][1000 genomes]
rs12032261	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12038299	0.83[EUR][1000 genomes]
rs12040633	0.89[CEU][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs12042503	0.85[EUR][1000 genomes]
rs12045776	0.95[EUR][1000 genomes]
rs12730520	0.95[EUR][1000 genomes]
rs12731254	0.93[EUR][1000 genomes]
rs12745879	0.84[EUR][1000 genomes]
rs12747926	0.88[EUR][1000 genomes]
rs17559050	0.95[EUR][1000 genomes]
rs17559134	0.81[JPT][hapmap]
rs2014441	0.95[EUR][1000 genomes]
rs2126389	1.00[CEU][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap];0.99[EUR][1000 genomes]
rs2169459	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34124959	0.98[EUR][1000 genomes]
rs35634773	0.95[EUR][1000 genomes]
rs3856161	0.96[EUR][1000 genomes]
rs4653644	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4653645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56280097	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59866505	0.85[EUR][1000 genomes]
rs61823593	0.95[EUR][1000 genomes]
rs61823594	0.95[EUR][1000 genomes]
rs61823595	0.95[EUR][1000 genomes]
rs61824002	0.82[EUR][1000 genomes]
rs6604731	0.84[GIH][hapmap]
rs6658752	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs6677956	0.94[EUR][1000 genomes]
rs6678103	0.89[CEU][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs6688246	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693324	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6702843	0.99[EUR][1000 genomes]
rs723999	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs745697	0.95[CEU][hapmap];0.84[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs7516059	0.99[EUR][1000 genomes]
rs7519753	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs7533614	0.95[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs7554109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9728094	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv1793921	chr1:224048131-224105965	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1817834	chr1:224052449-224095114	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1803377	chr1:224052449-224108920	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv522556	chr1:224061898-224075483	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12027539	RP11-504P24.3	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224063800-224064000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:224063800-224064200	ZNF genes & repeats	K562	blood

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