Variant report

Variant	rs6499231
Chromosome Location	chr16:69588016-69588017
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	chr16:69585478..69590758-chr16:69596695..69601394,7	MCF-7	breast:
2	chr16:69585327..69588068-chr16:69597880..69600088,2	K562	blood:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11075726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075729	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11640319	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11641686	0.99[ASN][1000 genomes]
rs11641722	0.99[ASN][1000 genomes]
rs11646575	0.91[EUR][1000 genomes]
rs11648335	0.91[ASN][1000 genomes]
rs1972659	0.91[EUR][1000 genomes]
rs2161630	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3848278	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4633710	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57497992	0.98[ASN][1000 genomes]
rs6499241	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7187634	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7191292	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7192543	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7204433	0.99[ASN][1000 genomes]
rs7205551	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8049728	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8055756	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8061052	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8061725	0.99[ASN][1000 genomes]
rs9302604	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783756	0.99[ASN][1000 genomes]
rs9938213	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6499231	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs6499231	CTD-2033A16.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69574600-69597800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:69587200-69589400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr16:69587600-69588200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr16:69587600-69588600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr16:69587600-69588600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr16:69588000-69588400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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