Variant report

Variant	rs9535832
Chromosome Location	chr13:52580329-52580330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52572621..52575296-chr13:52579187..52581060,2	K562	blood:
2	chr13:52573284..52575867-chr13:52579600..52581887,2	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1004576	0.91[CHB][hapmap]
rs1055062	0.91[CHB][hapmap]
rs1060631	0.91[CHB][hapmap]
rs11616964	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11620583	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12146904	0.91[CHB][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs12431310	0.91[CHB][hapmap]
rs1571189	0.91[CHB][hapmap]
rs1801243	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1886538	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1886542	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1886543	0.91[CHB][hapmap]
rs1886544	0.91[CHB][hapmap]
rs1886547	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1924611	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1998696	0.89[ASN][1000 genomes]
rs2004866	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2181891	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2274202	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2277448	0.91[CHB][hapmap]
rs2296347	0.91[CHB][hapmap]
rs2296348	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2296349	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2296350	0.81[ASN][1000 genomes]
rs2408544	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2408549	0.86[ASN][1000 genomes]
rs2408550	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2408551	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2408552	0.91[CHB][hapmap]
rs2408554	0.91[CHB][hapmap]
rs2408609	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2408611	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs28393037	0.80[ASN][1000 genomes]
rs2897964	0.91[CHB][hapmap]
rs2897976	0.80[ASN][1000 genomes]
rs2897977	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3368	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs35895576	0.93[ASN][1000 genomes]
rs3742289	0.91[CHB][hapmap]
rs3783242	0.91[CHB][hapmap]
rs3818422	0.91[CHB][hapmap]
rs3825528	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4297592	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4497567	0.91[CHB][hapmap]
rs4941727	0.91[CHB][hapmap]
rs55772266	0.83[ASN][1000 genomes]
rs61958812	0.86[ASN][1000 genomes]
rs6561656	0.91[CHB][hapmap]
rs6650383	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs723102	0.87[ASN][1000 genomes]
rs723103	0.87[ASN][1000 genomes]
rs732071	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7320831	0.91[CHB][hapmap]
rs7321120	0.91[CHB][hapmap]
rs7321435	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7324458	0.91[CHB][hapmap]
rs7327634	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7337430	0.93[ASN][1000 genomes]
rs747781	0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs755363	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7981904	0.91[CHB][hapmap]
rs7991237	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7993492	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994928	0.84[ASN][1000 genomes]
rs7995946	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7998770	0.91[CHB][hapmap]
rs9316563	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9526819	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9526821	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526823	0.91[CHB][hapmap]
rs9526825	0.91[CHB][hapmap]
rs9526837	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9526841	0.91[CHB][hapmap]
rs9526842	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9535812	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9535819	0.85[ASN][1000 genomes]
rs9535822	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535823	0.84[ASN][1000 genomes]
rs9535825	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs9535826	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535828	0.82[CEU][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs9535829	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535833	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535836	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs9535849	0.82[ASN][1000 genomes]
rs9535851	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9535856	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs9535858	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535860	0.85[ASN][1000 genomes]
rs9535861	0.82[CHB][hapmap]
rs9535862	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535866	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535867	0.91[CHB][hapmap]
rs9535872	0.81[ASN][1000 genomes]
rs9535873	0.91[CHB][hapmap]
rs9535878	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9535879	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535880	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535882	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9535885	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9535887	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs9563084	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9563089	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs9563091	0.82[ASN][1000 genomes]
rs9568682	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9568684	0.94[JPT][hapmap]
rs9568693	0.82[ASN][1000 genomes]
rs9568695	0.83[ASN][1000 genomes]
rs9568708	0.82[ASN][1000 genomes]
rs9568713	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	n/a
7	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9535832	CKAP2	cis	cerebellum	SCAN
rs9535832	NEK3	cis	cerebellum	SCAN
rs9535832	ALG11	cis	Muscle Skeletal	GTEx
rs9535832	CKAP2	cis	parietal	SCAN
rs9535832	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9535832	ATP7B	cis	cerebellum	SCAN
rs9535832	NCRNA00282	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52570800-52585000	Weak transcription	Colonic Mucosa	Colon
2	chr13:52570800-52585200	Weak transcription	Aorta	Aorta
3	chr13:52571000-52583800	Weak transcription	Brain Germinal Matrix	brain
4	chr13:52574000-52584400	Weak transcription	Fetal Stomach	stomach
5	chr13:52574200-52584400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:52574200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:52574400-52584400	Weak transcription	Psoas Muscle	Psoas
8	chr13:52574400-52584400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr13:52574400-52585000	Weak transcription	Left Ventricle	heart
10	chr13:52574400-52585200	Weak transcription	Lung	lung
11	chr13:52574600-52584400	Weak transcription	Fetal Brain Female	brain
12	chr13:52575400-52580400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr13:52575800-52581800	Weak transcription	K562	blood
14	chr13:52576400-52581400	Enhancers	Stomach Mucosa	stomach
15	chr13:52576800-52580400	Enhancers	Fetal Intestine Large	intestine
16	chr13:52578000-52584000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr13:52578400-52585200	Weak transcription	Pancreas	Pancrea
18	chr13:52578800-52580600	Genic enhancers	HepG2	liver
19	chr13:52578800-52584200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:52579000-52584000	Weak transcription	Brain Angular Gyrus	brain
21	chr13:52579200-52580600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:52579200-52580600	Weak transcription	Liver	Liver
23	chr13:52579200-52585000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr13:52579200-52585000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr13:52579200-52585200	Weak transcription	Gastric	stomach
26	chr13:52579400-52585000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr13:52579600-52580600	Enhancers	NHEK	skin
28	chr13:52579600-52580800	Flanking Active TSS	Fetal Intestine Small	intestine
29	chr13:52579600-52581200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr13:52579600-52581200	Enhancers	HMEC	breast
31	chr13:52579800-52580400	Active TSS	Duodenum Mucosa	Duodenum
32	chr13:52579800-52580600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:52579800-52581000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr13:52580000-52580600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:52580000-52580600	Weak transcription	Placenta	Placenta
36	chr13:52580200-52581000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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