Variant report

Variant	rs12884828
Chromosome Location	chr14:71674399-71674400
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71673720..71675748-chr14:71787192..71788845,2	MCF-7	breast:
2	chr14:71666330..71668532-chr14:71673021..71675504,2	MCF-7	breast:
3	chr14:71570510..71571060-chr14:71673984..71674688,2	K562	blood:
4	chr14:71673509..71676275-chr14:71679068..71681548,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000258517	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10129216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10136305	0.90[CHB][hapmap]
rs10139524	0.90[CHB][hapmap]
rs10141056	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10141170	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10145569	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10149204	0.90[CHB][hapmap]
rs11626879	0.87[ASN][1000 genomes]
rs11850277	0.90[CHB][hapmap]
rs12433619	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs12896453	0.85[CHB][hapmap]
rs2158532	0.90[CHB][hapmap]
rs2332539	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3742845	0.91[CHB][hapmap]
rs4899391	0.80[AMR][1000 genomes]
rs4902913	0.93[ASN][1000 genomes]
rs56193103	0.89[ASN][1000 genomes]
rs6574008	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145204	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757571	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8005382	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007420	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8023180	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71661200-71679400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:71669600-71677000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:71670200-71677200	Weak transcription	Spleen	Spleen
4	chr14:71673200-71674400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr14:71673200-71674400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:71673400-71674400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr14:71673400-71674600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr14:71673800-71674600	Enhancers	Brain Angular Gyrus	brain
9	chr14:71673800-71674800	Enhancers	Brain Cingulate Gyrus	brain
10	chr14:71674000-71676600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr14:71674000-71676600	Weak transcription	Brain Substantia Nigra	brain
12	chr14:71674000-71679200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:71674000-71680400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr14:71674200-71676600	Weak transcription	Brain Anterior Caudate	brain

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