Variant report

Variant	rs9316563
Chromosome Location	chr13:52555134-52555135
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52538063..52541078-chr13:52554449..52557060,3	K562	blood:
2	chr13:52546299..52549465-chr13:52553764..52557298,3	K562	blood:
3	chr13:52547935..52549465-chr13:52552409..52555264,2	K562	blood:
4	chr13:52549808..52551859-chr13:52553072..52555669,2	K562	blood:
5	chr13:52538417..52541078-chr13:52553924..52556751,2	K562	blood:

Variant related genes	Relation type
ENSG00000123191	Chromatin interaction
ENSG00000236044	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1004576	0.87[CHB][hapmap]
rs1055062	0.87[CHB][hapmap]
rs1060631	0.87[CHB][hapmap]
rs11616964	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11620583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12146904	0.86[CHB][hapmap]
rs12431310	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1571189	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1801243	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1801244	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs1886538	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1886542	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs1886543	0.87[CHB][hapmap]
rs1886544	0.87[CHB][hapmap]
rs1886547	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs1924611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951922	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1998696	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2004866	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147359	0.81[ASN][1000 genomes]
rs2147360	0.81[ASN][1000 genomes]
rs2181891	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274202	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2277448	0.87[CHB][hapmap]
rs2296347	0.87[CHB][hapmap]
rs2296348	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2296349	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2408544	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2408549	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2408550	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2408551	0.93[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2408552	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs2408554	0.87[CHB][hapmap]
rs2408609	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2408611	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2897964	0.86[CHB][hapmap]
rs2897977	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3368	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap]
rs35895576	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3742288	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs3742289	0.87[CHB][hapmap]
rs3783241	0.80[AMR][1000 genomes]
rs3783242	0.87[CHB][hapmap]
rs3818422	0.87[CHB][hapmap]
rs3825527	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs3825528	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4297592	0.93[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4497567	0.87[CHB][hapmap]
rs4600369	0.81[ASN][1000 genomes]
rs4941720	0.81[ASN][1000 genomes]
rs4941727	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs61958812	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6561656	0.87[CHB][hapmap]
rs723102	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs723103	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs732071	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7320831	0.87[CHB][hapmap]
rs7321120	0.87[CHB][hapmap]
rs7321435	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7324458	0.87[CHB][hapmap]
rs7327634	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7332272	0.83[ASN][1000 genomes]
rs7337430	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs747781	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs750290	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs755363	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs7981904	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs7991237	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs7993492	0.83[ASN][1000 genomes]
rs7994928	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7995946	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs7998770	0.87[CHB][hapmap]
rs7999812	0.82[CEU][hapmap];0.90[AMR][1000 genomes]
rs9526817	0.81[ASN][1000 genomes]
rs9526819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526821	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526823	0.87[CHB][hapmap]
rs9526825	0.87[CHB][hapmap]
rs9526832	0.81[EUR][1000 genomes]
rs9526837	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs9526841	0.87[CHB][hapmap]
rs9526842	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9535812	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535813	0.81[ASN][1000 genomes]
rs9535816	0.80[ASN][1000 genomes]
rs9535817	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535823	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535824	0.80[ASN][1000 genomes]
rs9535825	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9535826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535828	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535829	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535830	0.82[ASN][1000 genomes]
rs9535832	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9535833	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535836	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535851	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9535856	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs9535858	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9535860	0.81[EUR][1000 genomes]
rs9535862	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs9535866	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs9535867	0.87[CHB][hapmap]
rs9535873	0.87[CHB][hapmap]
rs9535878	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs9535879	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9535880	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9535882	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap]
rs9535885	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9535887	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs9563084	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9563089	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568681	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568682	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9568684	0.82[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs9568693	0.81[EUR][1000 genomes]
rs9568695	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9568713	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9316563	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
3	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:52544800-52556600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:52545000-52555400	Weak transcription	Adipose Nuclei	Adipose
8	chr13:52545000-52555600	Weak transcription	Aorta	Aorta
9	chr13:52545400-52555400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:52549000-52555400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr13:52549000-52555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:52551600-52555800	Enhancers	Fetal Intestine Small	intestine
13	chr13:52552600-52555800	Enhancers	Stomach Mucosa	stomach
14	chr13:52553000-52555800	Enhancers	Fetal Lung	lung
15	chr13:52553200-52556800	Enhancers	HepG2	liver
16	chr13:52553400-52555200	Weak transcription	Placenta	Placenta
17	chr13:52553400-52555400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr13:52553400-52555400	Weak transcription	Left Ventricle	heart
19	chr13:52553400-52555400	Weak transcription	Ovary	ovary
20	chr13:52553400-52555400	Weak transcription	Psoas Muscle	Psoas
21	chr13:52553400-52555400	Weak transcription	Right Atrium	heart
22	chr13:52553400-52556800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:52553400-52556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:52553400-52569400	Weak transcription	Pancreas	Pancrea
25	chr13:52553600-52555800	Enhancers	K562	blood
26	chr13:52554200-52556400	Enhancers	Placenta Amnion	Placenta Amnion
27	chr13:52554400-52555400	Weak transcription	Fetal Intestine Large	intestine
28	chr13:52554600-52555600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr13:52554800-52556000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:52554800-52556000	Flanking Active TSS	Fetal Heart	heart
31	chr13:52554800-52556400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:52555000-52555400	Active TSS	Right Ventricle	heart
33	chr13:52555000-52555400	Active TSS	HSMMtube	muscle
34	chr13:52555000-52555400	Enhancers	Osteobl	bone
35	chr13:52555000-52555800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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