Variant report

Variant	rs11616964
Chromosome Location	chr13:52581641-52581642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52578707..52580280-chr13:52581287..52584072,2	MCF-7	breast:
2	chr13:52580573..52584111-chr13:52584996..52587718,3	MCF-7	breast:
3	chr13:52576391..52578184-chr13:52580333..52583322,2	K562	blood:
4	chr13:52573284..52575867-chr13:52579600..52581887,2	K562	blood:

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11620583	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12584961	0.84[EUR][1000 genomes]
rs1801243	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1801244	0.82[AMR][1000 genomes]
rs1886542	0.85[ASN][1000 genomes]
rs1886547	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1924611	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1951922	0.88[AMR][1000 genomes]
rs1998696	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2004866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181891	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2274202	0.85[ASN][1000 genomes]
rs2296348	0.85[ASN][1000 genomes]
rs2296349	0.85[ASN][1000 genomes]
rs2296350	0.85[ASN][1000 genomes]
rs2408544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2408549	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2408550	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2408551	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2408609	0.85[ASN][1000 genomes]
rs2408611	0.85[ASN][1000 genomes]
rs28393037	0.85[ASN][1000 genomes]
rs2897976	0.85[ASN][1000 genomes]
rs2897977	0.85[ASN][1000 genomes]
rs3368	0.85[ASN][1000 genomes]
rs35895576	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742288	0.82[AMR][1000 genomes]
rs3825527	0.82[AMR][1000 genomes]
rs3825528	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4297592	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55772266	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61958812	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6650383	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs723102	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723103	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7327634	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7337430	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs750290	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs755363	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7993492	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7994928	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7995946	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7999812	0.82[AMR][1000 genomes]
rs9316563	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526819	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526832	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526837	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526842	0.83[ASN][1000 genomes]
rs9535812	0.88[AMR][1000 genomes]
rs9535817	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535819	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535822	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535823	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535826	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535828	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535829	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535830	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535832	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535836	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535849	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535851	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535858	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535860	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535862	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535866	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535872	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535878	0.85[ASN][1000 genomes]
rs9535879	0.85[ASN][1000 genomes]
rs9535880	0.85[ASN][1000 genomes]
rs9535885	0.83[ASN][1000 genomes]
rs9535887	0.83[ASN][1000 genomes]
rs9563084	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563089	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9563091	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9563093	0.83[ASN][1000 genomes]
rs9568681	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9568693	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568695	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568708	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568713	0.86[ASN][1000 genomes]

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	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	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
6	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
7	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11616964	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs11616964	ALG11	cis	Muscle Skeletal	GTEx

Chromatin state (count:37 , 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	chr13:52575800-52581800	Weak transcription	K562	blood
13	chr13:52578000-52584000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:52578400-52585200	Weak transcription	Pancreas	Pancrea
15	chr13:52578800-52584200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:52579000-52584000	Weak transcription	Brain Angular Gyrus	brain
17	chr13:52579200-52585000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:52579200-52585000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr13:52579200-52585200	Weak transcription	Gastric	stomach
20	chr13:52579400-52585000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr13:52580600-52581800	Flanking Active TSS	HepG2	liver
22	chr13:52580600-52584200	Enhancers	Liver	Liver
23	chr13:52580600-52584600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr13:52580600-52584800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:52580800-52582000	Enhancers	Fetal Intestine Large	intestine
26	chr13:52580800-52585000	Weak transcription	Placenta	Placenta
27	chr13:52581000-52584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:52581000-52584200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr13:52581000-52585200	Weak transcription	Spleen	Spleen
30	chr13:52581200-52581800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:52581200-52582200	Genic enhancers	Fetal Intestine Small	intestine
32	chr13:52581200-52584400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr13:52581200-52584600	Weak transcription	HMEC	breast
34	chr13:52581200-52585200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:52581400-52582800	Weak transcription	Stomach Mucosa	stomach
36	chr13:52581600-52581800	Enhancers	Brain Anterior Caudate	brain
37	chr13:52581600-52584000	Weak transcription	Duodenum Mucosa	Duodenum

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