Variant report

Variant	rs9536226
Chromosome Location	chr13:53244767-53244768
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53242611..53244232-chr13:53244626..53246224,2	MCF-7	breast:
2	chr13:53225240..53227958-chr13:53243712..53245830,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1436725	0.83[AFR][1000 genomes]
rs1978805	0.83[AFR][1000 genomes]
rs2033684	0.83[AFR][1000 genomes]
rs2033685	0.83[AFR][1000 genomes]
rs2257325	0.90[ASN][1000 genomes]
rs4539485	0.83[AFR][1000 genomes]
rs4542538	0.83[AFR][1000 genomes]
rs4884223	0.83[AFR][1000 genomes]
rs4884240	0.83[AFR][1000 genomes]
rs4885804	0.83[AFR][1000 genomes]
rs4885887	0.83[AFR][1000 genomes]
rs4885910	0.83[AFR][1000 genomes]
rs6561676	0.83[AFR][1000 genomes]
rs6561678	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6561679	0.83[AFR][1000 genomes]
rs7325840	0.83[AFR][1000 genomes]
rs7330193	0.83[AFR][1000 genomes]
rs7330361	0.83[AFR][1000 genomes]
rs7330755	0.83[AFR][1000 genomes]
rs7335270	0.83[AFR][1000 genomes]
rs7986540	0.83[AFR][1000 genomes]
rs7996692	0.83[AFR][1000 genomes]
rs7999466	0.83[AFR][1000 genomes]
rs9316581	0.83[AFR][1000 genomes]
rs9526970	0.83[AFR][1000 genomes]
rs9526978	0.83[AFR][1000 genomes]
rs9536189	0.90[ASN][1000 genomes]
rs9536228	0.83[AFR][1000 genomes]
rs9536235	0.83[AFR][1000 genomes]
rs9568748	0.83[AFR][1000 genomes]
rs9596671	0.83[AFR][1000 genomes]
rs971513	0.83[AFR][1000 genomes]
rs973198	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9536226	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53227800-53260000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:53228000-53251000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:53228200-53256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:53228400-53254600	Weak transcription	Colonic Mucosa	Colon
5	chr13:53228600-53254600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:53229000-53276600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:53229200-53247600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr13:53229200-53268000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:53229400-53254600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:53229800-53247600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:53229800-53255000	Weak transcription	Spleen	Spleen
12	chr13:53230200-53244800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr13:53230200-53247200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr13:53230200-53250600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:53230200-53263600	Weak transcription	Stomach Mucosa	stomach
16	chr13:53230400-53266400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr13:53230600-53245600	Strong transcription	HUVEC	blood vessel
18	chr13:53230600-53266400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr13:53230800-53253800	Weak transcription	Fetal Heart	heart
20	chr13:53230800-53277400	Weak transcription	Gastric	stomach
21	chr13:53231200-53246400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr13:53231200-53262400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr13:53231400-53245200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr13:53231600-53245200	Strong transcription	Liver	Liver
25	chr13:53231600-53246400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:53231600-53246600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr13:53231600-53247200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr13:53231800-53245200	Strong transcription	Osteobl	bone
29	chr13:53231800-53246200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:53231800-53247600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:53231800-53266400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr13:53232000-53247000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:53232200-53244800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:53232200-53247400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:53232200-53247600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:53232200-53247800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr13:53233200-53245000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:53234200-53246600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:53234400-53245000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr13:53234400-53245400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr13:53235200-53276000	Weak transcription	Right Ventricle	heart
42	chr13:53236600-53254600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr13:53236600-53255000	Weak transcription	Lung	lung
44	chr13:53236800-53254400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr13:53236800-53255000	Weak transcription	Aorta	Aorta
46	chr13:53237200-53261800	Weak transcription	Fetal Brain Male	brain
47	chr13:53237600-53250600	Weak transcription	Brain Germinal Matrix	brain
48	chr13:53237800-53249200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr13:53239000-53255600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:53239200-53249200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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