Variant report

Variant	rs12856726
Chromosome Location	chr13:52334619-52334620
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	chr13:52312271..52315134-chr13:52333689..52336005,2	K562	blood:

Variant related genes	Relation type
ENSG00000139668	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11619776	0.80[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1923875	1.00[ASW][hapmap]
rs6561644	0.82[MEX][hapmap]
rs7327107	0.82[MEX][hapmap]
rs7984225	0.82[MEX][hapmap]
rs7990679	0.82[MEX][hapmap]
rs9526792	0.82[MEX][hapmap]
rs9535713	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs9535767	0.82[ASW][hapmap]
rs9568642	0.95[MEX][hapmap];0.81[TSI][hapmap]
rs992583	0.82[MEX][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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12856726	FLJ13639	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
3	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:52322600-52337000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:52322600-52338200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:52322600-52338200	Weak transcription	Stomach Mucosa	stomach
7	chr13:52322600-52342200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:52322600-52342200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr13:52322800-52337600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:52322800-52338200	Weak transcription	HUVEC	blood vessel
11	chr13:52323000-52336400	Weak transcription	K562	blood
12	chr13:52323000-52336600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr13:52323000-52337200	Strong transcription	Primary B cells from cord blood	blood
14	chr13:52323000-52343400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr13:52323200-52335000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr13:52323200-52335400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:52323200-52336800	Strong transcription	Primary hematopoietic stem cells	blood
18	chr13:52323200-52337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:52323200-52338200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:52323200-52341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr13:52324200-52335400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:52324400-52335800	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr13:52324400-52337000	Strong transcription	HepG2	liver
24	chr13:52324400-52337200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr13:52324600-52336600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr13:52324600-52336800	Strong transcription	Primary T cells from cord blood	blood
27	chr13:52324600-52337400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:52324800-52335600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr13:52324800-52336800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr13:52324800-52337600	Strong transcription	Liver	Liver
31	chr13:52324800-52338200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr13:52324800-52342600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr13:52325400-52337800	Strong transcription	Thymus	Thymus
34	chr13:52325400-52338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr13:52325600-52335200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:52325600-52337600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr13:52326000-52342600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:52326200-52335000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr13:52326400-52336000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr13:52326600-52335800	Strong transcription	Osteobl	bone
41	chr13:52326600-52337000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr13:52327000-52337400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr13:52327600-52343200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr13:52327800-52337600	Strong transcription	NHEK	skin
45	chr13:52327800-52343000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr13:52328400-52336800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr13:52329000-52336600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:52329000-52337200	Strong transcription	Fetal Stomach	stomach
49	chr13:52329200-52335200	Strong transcription	Fetal Thymus	thymus
50	chr13:52329200-52337000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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