Variant report

Variant	rs2879485
Chromosome Location	chr1:152885913-152885914
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	chr1:152878367..152883347-chr1:152885450..152888334,6	MCF-7	breast:
2	chr1:152884643..152887047-chr1:152892229..152893780,2	K562	blood:

Variant related genes	Relation type
ENSG00000163207	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11205128	0.81[JPT][hapmap]
rs11205129	0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs11205130	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11205131	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11801996	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs11806470	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11807440	1.00[TSI][hapmap]
rs12021601	1.00[CEU][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs12022349	0.95[JPT][hapmap]
rs12022870	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs12024694	1.00[CEU][hapmap]
rs12028228	0.85[ASN][1000 genomes]
rs12034091	1.00[CEU][hapmap]
rs12036697	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12037754	1.00[CEU][hapmap]
rs12047630	1.00[CEU][hapmap]
rs12048655	0.95[JPT][hapmap]
rs12071483	1.00[TSI][hapmap]
rs12239808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12239814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406539	0.81[CHD][hapmap]
rs12568299	0.85[MEX][hapmap]
rs1611767	1.00[TSI][hapmap]
rs16834734	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs16834746	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16834751	1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap]
rs16834838	1.00[CEU][hapmap]
rs16834871	1.00[CEU][hapmap]
rs1854779	0.84[CHD][hapmap]
rs1974141	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1995307	1.00[CEU][hapmap]
rs2229496	0.82[CHD][hapmap]
rs2339383	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs2339398	0.84[MEX][hapmap]
rs2339501	1.00[CEU][hapmap]
rs2879484	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737862	1.00[CEU][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs3820136	0.82[CHD][hapmap]
rs3845340	0.89[ASN][1000 genomes]
rs4240863	1.00[CEU][hapmap]
rs4363387	0.95[JPT][hapmap]
rs4845325	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs4845494	0.95[JPT][hapmap]
rs58290373	0.83[ASN][1000 genomes]
rs6587711	0.80[ASN][1000 genomes]
rs6668295	0.87[ASN][1000 genomes]
rs7517189	0.82[CHD][hapmap]
rs7528862	0.81[CHD][hapmap]
rs7539232	0.84[CHD][hapmap]
rs7539610	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7552416	1.00[CEU][hapmap]
rs7553755	0.95[JPT][hapmap]
rs913996	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv998873	chr1:152869127-152975258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152883800-152886400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:152884200-152886400	Enhancers	HMEC	breast
3	chr1:152885000-152886000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:152885000-152886000	Enhancers	NHEK	skin

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