Variant report

Variant	rs2780314
Chromosome Location	chr14:36528492-36528493
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	chr14:36528201..36529761-chr14:36538388..36540318,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257585	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11156905	0.82[ASN][1000 genomes]
rs1333312	0.85[ASN][1000 genomes]
rs1333313	0.84[ASN][1000 genomes]
rs1742867	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1742868	0.85[CEU][hapmap]
rs1742869	0.85[CEU][hapmap]
rs1953119	0.84[ASN][1000 genomes]
rs1957313	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1957314	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2780312	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2780313	0.89[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs368181	0.85[CEU][hapmap]
rs371191	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs381529	0.83[ASN][1000 genomes]
rs394246	0.85[CEU][hapmap]
rs395212	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs395660	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs398467	0.91[ASN][1000 genomes]
rs398745	0.85[CEU][hapmap]
rs408558	0.96[ASN][1000 genomes]
rs408783	0.96[ASN][1000 genomes]
rs410546	0.95[ASN][1000 genomes]
rs429041	0.85[CEU][hapmap]
rs437723	0.94[ASN][1000 genomes]
rs448145	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6571735	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7145211	0.80[CEU][hapmap]
rs7145546	0.81[CEU][hapmap]
rs7147401	0.85[CEU][hapmap]
rs8003253	0.81[EUR][1000 genomes]
rs8007617	0.81[EUR][1000 genomes]
rs8007774	0.87[ASN][1000 genomes]
rs8008989	0.81[EUR][1000 genomes]
rs847514	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs847515	0.96[ASN][1000 genomes]
rs847516	0.82[EUR][1000 genomes]
rs860200	0.80[CEU][hapmap]
rs944290	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051045	chr14:36116503-36764947	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv542038	chr14:36116503-36764947	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1051147	chr14:36413342-36562863	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1040256	chr14:36501452-37172046	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv542040	chr14:36501452-37172046	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2780314	RP11-116N8.4	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:36523800-36530800	Weak transcription	Brain Substantia Nigra	brain
2	chr14:36524200-36530200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr14:36524200-36538200	Weak transcription	Brain Hippocampus Middle	brain
4	chr14:36526200-36535800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:36526800-36528800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr14:36527400-36529000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:36527800-36528600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr14:36528200-36528600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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