Variant report

Variant	rs12514280
Chromosome Location	chr5:52846416-52846417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52845985..52848173-chr5:52854524..52856886,2	K562	blood:
2	chr5:52845706..52848180-chr5:52855146..52856741,2	MCF-7	breast:
3	chr5:52845560..52852709-chr5:52853019..52860470,9	K562	blood:

Variant related genes	Relation type
ENSG00000164258	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10036570	0.87[ASN][1000 genomes]
rs10065003	0.90[ASN][1000 genomes]
rs10078892	0.83[ASN][1000 genomes]
rs10940322	0.82[ASN][1000 genomes]
rs10940323	0.85[ASN][1000 genomes]
rs12657948	0.85[ASN][1000 genomes]
rs13164833	0.87[ASN][1000 genomes]
rs13177321	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs1490769	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1532162	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs16881474	0.91[CHB][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs1844697	0.83[CHB][hapmap]
rs187658	0.82[CHB][hapmap]
rs189849	0.83[CHB][hapmap]
rs256081	0.83[CHB][hapmap]
rs256082	0.83[CHB][hapmap]
rs256093	0.83[CHB][hapmap]
rs256094	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs256098	0.83[CHB][hapmap]
rs256111	0.83[CHB][hapmap]
rs256118	0.87[CHB][hapmap]
rs2607478	0.82[CHB][hapmap]
rs2607485	0.83[CHB][hapmap]
rs2607506	0.82[CHB][hapmap]
rs2607508	0.82[CHB][hapmap]
rs2636993	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2637002	0.82[CHB][hapmap]
rs2637003	0.82[CHB][hapmap]
rs2637029	0.82[CHB][hapmap]
rs3103601	0.85[ASN][1000 genomes]
rs31308	0.82[CHB][hapmap]
rs365358	0.83[CHB][hapmap]
rs365578	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs366313	0.83[CHB][hapmap]
rs368461	0.83[CHB][hapmap]
rs372215	0.82[CHB][hapmap]
rs372370	0.82[ASN][1000 genomes]
rs377077	0.83[CHB][hapmap]
rs381575	0.82[CHB][hapmap]
rs392169	0.81[CHB][hapmap]
rs404838	0.82[CHB][hapmap]
rs409313	0.84[ASN][1000 genomes]
rs412559	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4147732	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs4147734	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs417550	0.82[CHB][hapmap]
rs425880	0.82[CHB][hapmap]
rs432020	0.83[CHB][hapmap]
rs435713	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs445347	0.83[CHB][hapmap]
rs451881	0.83[CHB][hapmap]
rs4865547	0.85[ASN][1000 genomes]
rs4865548	0.86[ASN][1000 genomes]
rs58889983	0.87[ASN][1000 genomes]
rs6864497	0.83[ASN][1000 genomes]
rs7711180	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs7717681	0.82[CHB][hapmap]
rs7736747	0.85[ASN][1000 genomes]
rs786334	0.83[CHB][hapmap]
rs918625	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs923610	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs9292024	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9790964	0.91[CHB][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9791019	0.88[ASN][1000 genomes]
rs9791152	0.89[ASN][1000 genomes]

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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12514280	NDUFS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52842600-52849000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:52843400-52848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:52843600-52848600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:52843600-52850600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:52844800-52848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52845000-52848800	Weak transcription	Stomach Mucosa	stomach
7	chr5:52846000-52848000	Weak transcription	K562	blood

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