Variant report

Variant	rs12585859
Chromosome Location	chr13:52396867-52396868
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	chr13:52389100..52392374-chr13:52395474..52400602,4	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10220242	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12584414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2031994	0.91[CEU][hapmap]
rs4354822	1.00[CEU][hapmap]
rs4941713	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943028	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56401568	0.94[ASN][1000 genomes]
rs621221	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7992588	0.85[CHB][hapmap]
rs878936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9591433	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9596586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596587	0.91[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9634846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs975504	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription 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 target site	33 gene(s)	inside rSNPs	diseases
9	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52389600-52398200	Weak transcription	Brain Substantia Nigra	brain
2	chr13:52389800-52397600	Weak transcription	Brain Hippocampus Middle	brain
3	chr13:52390200-52398200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:52392400-52404800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr13:52392600-52399600	Weak transcription	Fetal Lung	lung
6	chr13:52392800-52401800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr13:52393200-52397800	Enhancers	Fetal Muscle Leg	muscle
8	chr13:52393600-52406200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:52393600-52418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr13:52393800-52397800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr13:52393800-52398600	Weak transcription	Colon Smooth Muscle	Colon
12	chr13:52393800-52399200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr13:52393800-52399200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr13:52393800-52399200	Weak transcription	Adipose Nuclei	Adipose
15	chr13:52393800-52400000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:52394000-52399000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr13:52394000-52399000	Weak transcription	Right Atrium	heart
18	chr13:52394000-52399400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:52394000-52399600	Weak transcription	Left Ventricle	heart
20	chr13:52394000-52399800	Weak transcription	Right Ventricle	heart
21	chr13:52394200-52397800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr13:52394200-52399000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr13:52394200-52399800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:52394400-52398000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr13:52394600-52397000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:52394600-52400200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr13:52394800-52397800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:52395000-52397200	Enhancers	Fetal Heart	heart
29	chr13:52395000-52397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:52395000-52397600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:52395200-52397600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr13:52395200-52397600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr13:52395200-52397800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr13:52395200-52399200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr13:52395400-52397000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr13:52395600-52397200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr13:52395800-52397800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr13:52396000-52397800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr13:52396000-52398400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:52396000-52399200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:52396000-52400000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr13:52396200-52397000	Flanking Active TSS	Fetal Thymus	thymus
43	chr13:52396200-52398400	Enhancers	Brain Anterior Caudate	brain
44	chr13:52396400-52397400	Enhancers	Fetal Muscle Trunk	muscle
45	chr13:52396400-52399200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr13:52396600-52397600	Enhancers	Spleen	Spleen
47	chr13:52396600-52398000	Enhancers	Primary B cells from peripheral blood	blood
48	chr13:52396600-52398200	Enhancers	Primary hematopoietic stem cells	blood
49	chr13:52396600-52399600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr13:52396600-52400400	Weak transcription	Rectal Mucosa Donor 31	rectum

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