Variant report

Variant	rs3925516
Chromosome Location	chr5:178062743-178062744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178053909..178055898-chr5:178062249..178064358,2	MCF-7	breast:
2	chr5:178056861..178059158-chr5:178059957..178062888,3	MCF-7	breast:
3	chr5:178052435..178056379-chr5:178060810..178069102,10	MCF-7	breast:
4	chr5:178051700..178056905-chr5:178058361..178063297,6	K562	blood:
5	chr5:178051406..178054031-chr5:178060222..178062743,2	K562	blood:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10903228	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952857	0.92[ASN][1000 genomes]
rs11954313	1.00[ASN][1000 genomes]
rs11954316	1.00[ASN][1000 genomes]
rs11954364	1.00[ASN][1000 genomes]
rs12187704	0.81[AFR][1000 genomes]
rs174438	0.85[ASN][1000 genomes]
rs262014	1.00[CHD][hapmap]
rs262037	1.00[CHB][hapmap]
rs262054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs262055	1.00[CHB][hapmap]
rs262057	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs262061	1.00[CHB][hapmap]
rs262064	1.00[CHB][hapmap]
rs262070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4473788	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4557432	0.83[AMR][1000 genomes]
rs4639246	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560842	0.83[AMR][1000 genomes]
rs6866974	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871372	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889322	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73346597	0.92[ASN][1000 genomes]
rs7716274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7718720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs775700	0.82[MEX][hapmap]

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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178059600-178064000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:178061600-178063200	Enhancers	HMEC	breast
3	chr5:178061600-178063400	Enhancers	Placenta	Placenta
4	chr5:178062000-178062800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:178062200-178062800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:178062200-178062800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:178062200-178062800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:178062200-178063400	Enhancers	NHEK	skin
9	chr5:178062600-178064400	Weak transcription	HepG2	liver

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