Variant report

Variant	rs1549287
Chromosome Location	chr16:69590366-69590367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69458413..69461284-chr16:69590262..69592868,2	MCF-7	breast:
2	chr16:69585478..69590758-chr16:69596695..69601394,7	MCF-7	breast:
3	chr16:69588513..69590779-chr16:69598119..69599753,2	K562	blood:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000103018	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1043470	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs11644997	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465451	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168637	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17298067	0.83[ASN][1000 genomes]
rs17299478	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs190282	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1972658	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs244416	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs244419	0.81[AMR][1000 genomes]
rs244422	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs244423	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33060	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33061	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs33062	0.84[AMR][1000 genomes]
rs33063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4783720	0.89[EUR][1000 genomes]
rs62049971	0.85[AMR][1000 genomes]
rs62052820	0.96[ASN][1000 genomes]
rs7193778	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7200764	0.80[EUR][1000 genomes]
rs72783112	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8048032	0.83[EUR][1000 genomes]
rs8062941	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1549287	ACD	cis	parietal	SCAN
rs1549287	NFAT5	cis	cerebellum	SCAN
rs1549287	CHST4	cis	cerebellum	SCAN
rs1549287	LOC283970	cis	multi-tissue	Pritchard
rs1549287	LCAT	cis	cerebellum	SCAN

Chromatin state (count:4 , 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	chr16:69589800-69592400	Weak transcription	GM12878-XiMat	blood
3	chr16:69589800-69596800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:69590000-69597800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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