Variant report

Variant	rs9536242
Chromosome Location	chr13:53277098-53277099
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1057478	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1924036	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2038826	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2147676	0.83[CHB][hapmap]
rs2147692	0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs2575960	0.85[CHB][hapmap]
rs2760815	0.83[CEU][hapmap]
rs3742297	0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs4284531	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4884235	0.85[CHB][hapmap]
rs61959657	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7139495	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7139630	0.85[CHB][hapmap]
rs7328729	0.85[CHB][hapmap]
rs7334137	0.85[CHB][hapmap]
rs7334677	0.85[CHB][hapmap]
rs7336771	0.85[CHB][hapmap]
rs9526950	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9526968	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9526974	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs9526975	0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs9526979	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536123	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9536185	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9536190	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9536199	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9536203	1.00[LWK][hapmap];0.96[MKK][hapmap]
rs9536204	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536211	0.86[JPT][hapmap]
rs9536212	0.93[JPT][hapmap]
rs9536219	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs9536220	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9536236	0.81[EUR][1000 genomes]
rs9536262	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9563113	0.85[CHB][hapmap]
rs9563114	0.85[CHB][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9536242	CKAP2	cis	Nerve Tibial	GTEx
rs9536242	CKAP2	cis	Thyroid	GTEx
rs9536242	CKAP2	cis	parietal	SCAN
rs9536242	HNRNPA1L2	cis	cerebellum	SCAN
rs9536242	SUGT1	cis	cerebellum	SCAN
rs9536242	CKAP2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53230800-53277400	Weak transcription	Gastric	stomach
2	chr13:53242800-53278600	Weak transcription	Psoas Muscle	Psoas
3	chr13:53255800-53277600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:53256000-53282600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr13:53256600-53297800	Weak transcription	Pancreas	Pancrea
6	chr13:53260000-53277600	Weak transcription	Brain Hippocampus Middle	brain
7	chr13:53260200-53277600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:53260400-53279200	Weak transcription	Aorta	Aorta
9	chr13:53260800-53280400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:53260800-53297000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr13:53261000-53285200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:53262600-53285600	Weak transcription	HMEC	breast
13	chr13:53262800-53277800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr13:53263000-53281800	Weak transcription	Fetal Brain Male	brain
15	chr13:53263400-53277200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr13:53263400-53277800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:53263400-53278200	Weak transcription	Fetal Lung	lung
18	chr13:53263400-53285400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:53265200-53277600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr13:53266400-53277200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr13:53267600-53277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr13:53270000-53278200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:53270800-53282400	Weak transcription	Fetal Brain Female	brain
24	chr13:53272400-53297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr13:53273200-53279200	Weak transcription	Left Ventricle	heart
26	chr13:53274200-53285400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr13:53274400-53279200	Weak transcription	Liver	Liver
28	chr13:53274800-53277200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr13:53275000-53278600	Weak transcription	HSMM	muscle
30	chr13:53275000-53278800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr13:53275200-53277200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:53275200-53278400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:53275200-53278800	Enhancers	Primary hematopoietic stem cells	blood
34	chr13:53275400-53279400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:53275400-53280200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr13:53275800-53277200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr13:53275800-53277400	Enhancers	HUVEC	blood vessel
38	chr13:53275800-53278200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:53276000-53278400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr13:53276200-53284600	Weak transcription	Fetal Muscle Leg	muscle
41	chr13:53276400-53278400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr13:53276600-53277200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr13:53276600-53277200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr13:53276800-53279000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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