Variant report

Variant	rs11672446
Chromosome Location	chr19:51763357-51763358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr19:51762562-51763410	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:51661388..51662622-chr19:51761876..51763512,12	MCF-7	breast:
2	chr19:51762812..51764543-chr19:51765982..51768235,3	K562	blood:

Variant related genes	Relation type
SIGLECL1	TF binding region
ENSG00000179213	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1034521	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10402797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10406897	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10412123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10412214	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10414689	1.00[CEU][hapmap]
rs11084061	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11084062	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11084063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11084064	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461282	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12461354	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1319675	0.86[ASN][1000 genomes]
rs1501447	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1501448	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1501449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566578	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17801843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1803254	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34606577	0.86[ASN][1000 genomes]
rs7253831	0.86[ASN][1000 genomes]
rs7256372	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256512	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73612300	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8103085	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9676731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs989502	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs989504	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv518134	chr19:51750238-51765953	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1060026	chr19:51751123-51773175	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51762600-51772600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:51762800-51767200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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