Variant report

Variant	rs10407039
Chromosome Location	chr19:52183884-52183885
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	chr19:52175247..52176993-chr19:52183219..52185432,2	MCF-7	breast:
2	chr19:52176923..52179869-chr19:52183377..52186044,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10406015	0.84[EUR][1000 genomes]
rs10408696	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10412972	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap]
rs10421946	0.96[ASN][1000 genomes]
rs10853838	0.96[ASN][1000 genomes]
rs11084102	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11084105	1.00[EUR][1000 genomes]
rs11084107	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609218	0.92[ASN][1000 genomes]
rs12972030	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972881	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974001	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12981272	0.96[ASN][1000 genomes]
rs12981705	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981813	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982077	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983624	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986275	0.93[EUR][1000 genomes]
rs2034574	0.91[ASN][1000 genomes]
rs2034576	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];1.00[EUR][1000 genomes]
rs2053926	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2167415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167422	0.96[ASN][1000 genomes]
rs2167423	0.95[ASN][1000 genomes]
rs2864916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59485321	0.81[ASN][1000 genomes]
rs62106945	0.86[EUR][1000 genomes]
rs66465936	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517831	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67111559	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67501025	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67926871	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67932802	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68072667	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254012	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254491	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254536	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254881	1.00[EUR][1000 genomes]
rs7255046	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255069	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257958	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258702	1.00[EUR][1000 genomes]
rs74176147	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74176148	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8108345	0.95[ASN][1000 genomes]
rs8111426	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	nsv2532	chr19:52109105-52186946	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
13	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking 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	518 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52181600-52184600	Weak transcription	Right Atrium	heart
2	chr19:52182200-52184200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:52183600-52184600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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