Variant report

Variant	rs4539371
Chromosome Location	chr12:60242912-60242913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:60240866..60243089-chr12:60312800..60315129,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10877352	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173169	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173170	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173171	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173189	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173197	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173199	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11173200	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173201	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173202	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12049943	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230605	0.83[AMR][1000 genomes]
rs12298637	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650311	0.86[ASW][hapmap]
rs2365314	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2365315	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35218918	0.83[EUR][1000 genomes]
rs35971116	0.82[EUR][1000 genomes]
rs4387384	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412789	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417320	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623939	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758741	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758846	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56098460	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7975905	0.84[EUR][1000 genomes];0.84[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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899134	chr12:60141518-60263723	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4539371	KIF5A	cis	cerebellum	SCAN
rs4539371	AVIL	cis	cerebellum	SCAN
rs4539371	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs4539371	ERBB3	cis	parietal	SCAN
rs4539371	GPR84	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60239200-60243800	Weak transcription	HUVEC	blood vessel
2	chr12:60240600-60243000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:60242200-60295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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