Variant report

Variant	rs9536220
Chromosome Location	chr13:53227834-53227835
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:53189348..53193688-chr13:53225267..53228139,8	MCF-7	breast:
2	chr13:53215104..53217509-chr13:53226480..53228845,2	K562	blood:
3	chr13:53226555..53228977-chr13:53419370..53422779,3	MCF-7	breast:
4	chr13:53215104..53218356-chr13:53226198..53228845,3	K562	blood:
5	chr13:53023588..53025754-chr13:53225469..53228375,2	K562	blood:

Variant related genes	Relation type
ENSG00000250299	Chromatin interaction
ENSG00000136099	Chromatin interaction
ENSG00000139675	Chromatin interaction
ENSG00000136100	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1057478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11616261	0.87[AFR][1000 genomes]
rs11616459	0.83[CHB][hapmap]
rs1924036	0.83[CHB][hapmap]
rs2038826	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2147676	0.81[CHB][hapmap]
rs2147692	0.83[CHB][hapmap];0.90[YRI][hapmap]
rs2575960	0.83[CHB][hapmap]
rs2760815	0.90[CEU][hapmap]
rs3742297	0.83[CHB][hapmap];0.90[YRI][hapmap]
rs3892337	0.82[YRI][hapmap]
rs4284531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4884235	0.83[CHB][hapmap]
rs61959657	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7139495	0.83[CHB][hapmap]
rs7139630	0.83[CHB][hapmap]
rs7328729	0.83[CHB][hapmap]
rs7334137	0.83[CHB][hapmap]
rs7334677	0.83[CHB][hapmap]
rs7336771	0.83[CHB][hapmap]
rs9526950	0.84[ASN][1000 genomes]
rs9526968	0.82[CHB][hapmap]
rs9526974	0.83[CHB][hapmap]
rs9526975	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9526979	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9536079	0.81[YRI][hapmap]
rs9536104	0.83[CHB][hapmap]
rs9536123	0.83[CHB][hapmap]
rs9536185	0.95[ASN][1000 genomes]
rs9536190	0.95[ASN][1000 genomes]
rs9536199	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9536204	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536211	0.82[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs9536212	0.89[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes]
rs9536219	0.83[CHB][hapmap]
rs9536242	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9536262	0.83[CHB][hapmap];0.89[YRI][hapmap]
rs9563113	0.83[CHB][hapmap]
rs9563114	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9536220	CKAP2	cis	Thyroid	GTEx
rs9536220	CKAP2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53224400-53228600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr13:53224600-53228600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr13:53224600-53229200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr13:53224800-53228400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr13:53225000-53228000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr13:53225000-53228200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr13:53225000-53228200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:53225000-53228200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:53225000-53228200	Active TSS	NHDF-Ad	bronchial
10	chr13:53225000-53228400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr13:53225000-53228400	Active TSS	Fetal Intestine Small	intestine
12	chr13:53225000-53228600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr13:53225000-53228600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr13:53225000-53229000	Active TSS	K562	blood
15	chr13:53225000-53229400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:53225200-53228000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:53225200-53228000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr13:53225200-53228000	Active TSS	Fetal Kidney	kidney
19	chr13:53225200-53228000	Active TSS	Fetal Stomach	stomach
20	chr13:53225200-53228200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:53225200-53228200	Active TSS	Colonic Mucosa	Colon
22	chr13:53225200-53228200	Active TSS	GM12878-XiMat	blood
23	chr13:53225200-53228200	Active TSS	HSMM	muscle
24	chr13:53225200-53228400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:53225200-53228400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr13:53225200-53228400	Active TSS	Fetal Intestine Large	intestine
27	chr13:53225200-53228400	Active TSS	Fetal Muscle Trunk	muscle
28	chr13:53225200-53228400	Active TSS	A549	lung
29	chr13:53225200-53228600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:53225200-53228600	Active TSS	Hela-S3	cervix
31	chr13:53225400-53228000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:53225400-53228000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr13:53225400-53228000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:53225400-53228000	Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:53225400-53228000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr13:53225400-53228000	Active TSS	Fetal Brain Male	brain
37	chr13:53225400-53228000	Active TSS	Fetal Heart	heart
38	chr13:53225400-53228000	Active TSS	Fetal Lung	lung
39	chr13:53225400-53228000	Active TSS	Fetal Thymus	thymus
40	chr13:53225400-53228000	Active TSS	Thymus	Thymus
41	chr13:53225400-53228000	Active TSS	NH-A	brain
42	chr13:53225400-53228200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:53225400-53228200	Active TSS	Right Ventricle	heart
44	chr13:53225400-53228200	Active TSS	HMEC	breast
45	chr13:53225400-53228200	Active TSS	NHEK	skin
46	chr13:53225400-53228400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr13:53225400-53228400	Active TSS	Aorta	Aorta
48	chr13:53225400-53228400	Active TSS	Right Atrium	heart
49	chr13:53225400-53228400	Active TSS	HSMMtube	muscle
50	chr13:53225400-53228800	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links