Variant report

Variant	rs17006054
Chromosome Location	chr3:19584985-19584986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:19390113..19391205-chr3:19584358..19585952,11	MCF-7	breast:
2	chr3:19106420..19107155-chr3:19584445..19585029,2	MCF-7	breast:
3	chr3:19390558..19391094-chr3:19584541..19585367,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510495	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11543540	0.83[ASN][1000 genomes]
rs11561668	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17005972	0.94[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs17005976	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs17005980	0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs17005998	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17006003	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17006010	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17006048	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs17006062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57272811	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57684768	0.88[ASN][1000 genomes]
rs58996643	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60546560	0.86[ASN][1000 genomes]
rs60566663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60777133	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60942804	0.86[ASN][1000 genomes]
rs61579329	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6781615	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6800537	0.83[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6801951	0.85[JPT][hapmap]
rs7614599	0.85[ASN][1000 genomes]
rs7617994	0.91[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7626734	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7626907	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649671	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653865	0.84[ASN][1000 genomes]
rs951678	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv948636	chr3:19335802-19856585	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3386719	chr3:19454588-19895807	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv876595	chr3:19512074-19726308	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1009097	chr3:19539647-19787978	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv1833163	chr3:19547184-19861406	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv1830352	chr3:19549745-19856837	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv1829505	chr3:19554497-19754793	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	esv1833282	chr3:19554497-19849542	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19578000-19585600	Enhancers	Primary B cells from peripheral blood	blood
2	chr3:19583200-19586000	Enhancers	GM12878-XiMat	blood
3	chr3:19583400-19585000	Enhancers	Primary hematopoietic stem cells	blood
4	chr3:19584200-19585000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:19584400-19585000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr3:19584600-19585000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:19584600-19585400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:19584800-19586400	Enhancers	Primary B cells from cord blood	blood
9	chr3:19584800-19588600	Weak transcription	Rectal Mucosa Donor 29	rectum

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