Variant report

Variant	rs9535895
Chromosome Location	chr13:52765847-52765848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1327323	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1815348	0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs1815349	0.81[ASN][1000 genomes]
rs1815350	0.81[ASN][1000 genomes]
rs1865877	0.83[ASN][1000 genomes]
rs1887360	0.87[ASN][1000 genomes]
rs2760772	0.86[ASN][1000 genomes]
rs3866534	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3886077	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs4369550	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4545703	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs4884452	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs56033750	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61957257	0.83[EUR][1000 genomes]
rs6561665	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7981050	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7983971	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7987115	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7993748	0.82[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap]
rs9535914	0.93[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9536046	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9536048	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9536052	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9596643	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9596648	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9596651	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv976116	chr13:52741751-52768674	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535895	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9535895	CKAP2	cis	Artery Tibial	GTEx
rs9535895	CKAP2	cis	Nerve Tibial	GTEx
rs9535895	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9535895	CKAP2	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52734400-52768000	Weak transcription	Aorta	Aorta
2	chr13:52734600-52766000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr13:52736400-52767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:52737200-52767400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr13:52738400-52767400	Weak transcription	HMEC	breast
6	chr13:52740000-52767200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr13:52741000-52767800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:52743400-52767600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:52743400-52767800	Weak transcription	Esophagus	oesophagus
10	chr13:52743400-52768200	Weak transcription	Small Intestine	intestine
11	chr13:52745600-52767400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr13:52747400-52767200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr13:52752600-52767200	Weak transcription	Psoas Muscle	Psoas
14	chr13:52754400-52767200	Weak transcription	Colonic Mucosa	Colon
15	chr13:52754400-52767800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr13:52754600-52766000	Weak transcription	Fetal Lung	lung
17	chr13:52754600-52767000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:52754600-52767200	Weak transcription	Fetal Kidney	kidney
19	chr13:52754600-52767200	Weak transcription	NHEK	skin
20	chr13:52754600-52767400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:52754600-52767400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:52754600-52767400	Weak transcription	Right Ventricle	heart
23	chr13:52754600-52767400	Weak transcription	NHDF-Ad	bronchial
24	chr13:52754600-52767800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:52754600-52767800	Weak transcription	Lung	lung
26	chr13:52755600-52767400	Weak transcription	HUVEC	blood vessel
27	chr13:52758000-52768000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr13:52758600-52767000	Weak transcription	Primary B cells from cord blood	blood
29	chr13:52758600-52767400	Weak transcription	A549	lung
30	chr13:52758600-52767600	Weak transcription	Placenta	Placenta
31	chr13:52758600-52767800	Weak transcription	Spleen	Spleen
32	chr13:52758800-52767000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:52759000-52767200	Weak transcription	Colon Smooth Muscle	Colon
34	chr13:52759000-52767400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:52759200-52767800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:52759200-52767800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr13:52759600-52767400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr13:52760200-52766800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:52760200-52767200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:52760200-52767400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:52760200-52767400	Weak transcription	Fetal Stomach	stomach
42	chr13:52760200-52767400	Weak transcription	Thymus	Thymus
43	chr13:52760400-52766000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:52760400-52767000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr13:52760400-52767200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr13:52760400-52767400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr13:52760400-52767400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:52760400-52767400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr13:52760400-52767400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr13:52760400-52767800	Weak transcription	Gastric	stomach

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