Variant report

Variant	rs9562941
Chromosome Location	chr13:50509784-50509785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50509071..50511034-chr13:50570092..50572951,3	K562	blood:
2	chr13:50365136..50367359-chr13:50509492..50511604,3	MCF-7	breast:
3	chr13:50507293..50510312-chr13:50568081..50571220,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11617754	0.82[CHB][hapmap]
rs12429041	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12429047	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12430021	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12430731	0.86[ASN][1000 genomes]
rs12584761	0.91[EUR][1000 genomes]
rs12585937	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1609571	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17073758	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2407879	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2897794	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142286	0.89[EUR][1000 genomes]
rs4942896	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942898	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942903	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs790943	0.82[CHB][hapmap]
rs7983585	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9562938	0.84[ASN][1000 genomes]
rs9562939	0.83[ASN][1000 genomes]
rs9562940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562944	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562951	0.95[EUR][1000 genomes]
rs9568348	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568351	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568353	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568357	0.82[CHB][hapmap]
rs9568359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568365	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568366	0.81[CHB][hapmap]
rs9568371	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568379	0.91[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	esv1836423	chr13:50509784-50514706	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1836704	chr13:50509784-50514706	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1838605	chr13:50509784-50514706	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50489200-50510000	Weak transcription	Spleen	Spleen
2	chr13:50500000-50509800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:50502600-50509800	Weak transcription	Gastric	stomach
4	chr13:50508800-50509800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:50508800-50509800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr13:50508800-50509800	Flanking Active TSS	Osteobl	bone
7	chr13:50508800-50510400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:50508800-50511400	Active TSS	Right Atrium	heart
9	chr13:50509000-50509800	Weak transcription	Small Intestine	intestine
10	chr13:50509000-50510000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:50509000-50510800	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr13:50509000-50511400	Active TSS	A549	lung
13	chr13:50509000-50511400	Active TSS	K562	blood
14	chr13:50509000-50511600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:50509000-50511600	Active TSS	HMEC	breast
16	chr13:50509000-50511800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:50509200-50509800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr13:50509200-50509800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:50509200-50509800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr13:50509200-50510000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr13:50509200-50510200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr13:50509200-50511400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:50509400-50509800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:50509400-50509800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr13:50509400-50509800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr13:50509400-50509800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr13:50509400-50509800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr13:50509400-50509800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr13:50509400-50509800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr13:50509400-50509800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr13:50509400-50509800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr13:50509400-50509800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr13:50509400-50509800	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr13:50509400-50509800	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr13:50509400-50509800	Flanking Active TSS	Fetal Brain Female	brain
36	chr13:50509400-50509800	Flanking Active TSS	Fetal Heart	heart
37	chr13:50509400-50509800	Flanking Active TSS	Fetal Stomach	stomach
38	chr13:50509400-50509800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr13:50509400-50509800	Bivalent/Poised TSS	Thymus	Thymus
40	chr13:50509400-50509800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr13:50509400-50510000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr13:50509400-50510000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr13:50509400-50510000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr13:50509400-50510000	Flanking Active TSS	Liver	Liver
45	chr13:50509400-50510000	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr13:50509400-50510000	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr13:50509400-50510000	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr13:50509400-50510000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr13:50509400-50510000	Flanking Active TSS	HUVEC	blood vessel
50	chr13:50509400-50510200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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