Variant report

Variant	rs17226809
Chromosome Location	chr13:39584916-39584917
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39584395..39587085-chr13:39611673..39614003,2	MCF-7	breast:
2	chr13:39583306..39585732-chr13:39594165..39596602,2	K562	blood:

Variant related genes	Relation type
ENSG00000188811	Chromatin interaction
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12428338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12428487	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12429615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430798	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12431010	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12431083	1.00[AFR][1000 genomes]
rs12431327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1575886	1.00[AFR][1000 genomes]
rs17226184	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17226219	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17235076	1.00[AFR][1000 genomes]
rs17235139	1.00[AFR][1000 genomes]
rs17826253	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs41286135	1.00[AFR][1000 genomes]
rs41286945	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv977227	chr13:39584329-39585449	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39574600-39585000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:39579000-39585000	Weak transcription	Gastric	stomach
3	chr13:39580200-39585000	Weak transcription	Fetal Stomach	stomach
4	chr13:39580200-39585000	Weak transcription	NH-A	brain
5	chr13:39580400-39585000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr13:39580400-39585000	Weak transcription	Lung	lung
7	chr13:39580800-39586200	Weak transcription	Colonic Mucosa	Colon
8	chr13:39581200-39585000	Weak transcription	Aorta	Aorta
9	chr13:39581200-39585000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:39581200-39585000	Weak transcription	Thymus	Thymus
11	chr13:39581400-39585400	Weak transcription	Fetal Intestine Small	intestine
12	chr13:39581600-39585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr13:39581600-39590800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:39581600-39592000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:39581600-39592400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:39581800-39585000	Weak transcription	Esophagus	oesophagus
17	chr13:39581800-39585000	Weak transcription	Spleen	Spleen
18	chr13:39581800-39585400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:39581800-39589400	Strong transcription	Brain Germinal Matrix	brain
20	chr13:39581800-39592200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:39581800-39593200	Strong transcription	HSMM	muscle
22	chr13:39581800-39597000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:39582000-39585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr13:39582000-39585000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:39582000-39588000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr13:39582000-39596600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:39582200-39590800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr13:39582200-39592600	Strong transcription	Fetal Thymus	thymus
30	chr13:39582200-39593400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr13:39582200-39596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr13:39582200-39596800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:39582200-39597400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:39582400-39585000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr13:39582400-39590400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr13:39582400-39590400	Strong transcription	GM12878-XiMat	blood
37	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr13:39582600-39586000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr13:39582600-39589600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr13:39582600-39592000	Strong transcription	Placenta	Placenta
41	chr13:39582600-39592400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr13:39582600-39592400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr13:39582800-39593600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr13:39583000-39585000	Weak transcription	Primary T cells from cord blood	blood
45	chr13:39583000-39585400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr13:39583000-39585400	Weak transcription	Right Ventricle	heart
47	chr13:39583000-39592400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:39583200-39585000	Weak transcription	Pancreas	Pancrea
49	chr13:39583200-39592400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:39583200-39592400	Strong transcription	Primary B cells from peripheral blood	blood

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