Variant report

Variant	rs12590112
Chromosome Location	chr14:35364015-35364016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35357879..35360041-chr14:35362909..35365006,2	K562	blood:
2	chr14:35342299..35344580-chr14:35362936..35364444,2	K562	blood:
3	chr14:35363874..35366467-chr14:35451081..35453082,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258704	Chromatin interaction
ENSG00000100883	Chromatin interaction
ENSG00000198604	Chromatin interaction
ENSG00000258738	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10136352	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10150083	0.94[JPT][hapmap]
rs1200414	0.90[JPT][hapmap]
rs12431818	0.90[JPT][hapmap]
rs12433706	0.84[CEU][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs12435778	0.90[JPT][hapmap]
rs12587021	0.89[JPT][hapmap]
rs13379337	0.94[CHD][hapmap];0.89[JPT][hapmap]
rs17102726	0.90[JPT][hapmap]
rs17102768	0.90[JPT][hapmap]
rs17102795	0.89[JPT][hapmap]
rs17102829	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17526787	0.84[CEU][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2383677	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs34072166	0.90[JPT][hapmap]
rs35713265	0.89[ASN][1000 genomes]
rs3783315	0.90[JPT][hapmap];0.85[TSI][hapmap]
rs3783316	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs7148400	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7150069	0.89[JPT][hapmap]
rs7153289	1.00[JPT][hapmap]
rs8005470	0.90[JPT][hapmap]
rs8005659	0.94[CHD][hapmap];0.89[JPT][hapmap]
rs8010579	0.90[JPT][hapmap]
rs8019856	0.81[JPT][hapmap]

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	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1045939	chr14:35311074-35494703	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	esv20720	chr14:35362907-35374689	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12590112	NUBPL	cis	parietal	SCAN
rs12590112	SCFD1	cis	cerebellum	SCAN
rs12590112	SNX6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35364000-35365600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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