Variant report

Variant	rs9535879
Chromosome Location	chr13:52704624-52704625
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52701771..52705558-chr13:52767896..52769871,3	MCF-7	breast:
2	chr13:52376747..52380251-chr13:52704508..52706445,3	MCF-7	breast:
3	chr13:52699126..52701652-chr13:52702989..52705135,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UTP14C-1	chr13:52703031-52706193	NR_110306
2	lnc-UTP14C-1	chr13:52703027-52706193	NONHSAT033962

Variant related genes	Relation type
ENSG00000231856	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000243406	Chromatin interaction
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1004576	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1055062	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1060631	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs11616964	0.85[ASN][1000 genomes]
rs11620583	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs12146904	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs12431310	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12584961	0.85[ASN][1000 genomes]
rs1571189	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs1801243	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs1886538	0.80[CHB][hapmap]
rs1886542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886543	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1886544	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1886547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs1924611	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1998696	0.91[ASN][1000 genomes]
rs2004866	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2181891	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs2274202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277448	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2296347	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2296348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296350	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs2408549	0.94[ASN][1000 genomes]
rs2408550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2408551	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2408552	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2408554	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2408609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393037	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897964	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2897976	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35895576	0.87[ASN][1000 genomes]
rs3742289	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs3783242	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs3818422	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs3825528	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4297592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4497567	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs4941727	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs55772266	0.94[ASN][1000 genomes]
rs61958812	0.94[ASN][1000 genomes]
rs6561656	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs6561658	0.92[CEU][hapmap]
rs6650383	0.90[ASN][1000 genomes]
rs66849828	0.81[EUR][1000 genomes]
rs723102	0.93[ASN][1000 genomes]
rs723103	0.93[ASN][1000 genomes]
rs732071	0.80[CHB][hapmap]
rs7320831	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7321120	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7321435	0.80[CHB][hapmap]
rs7324458	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7327634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7337430	0.87[ASN][1000 genomes]
rs747781	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs755363	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7981904	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7991237	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7993492	0.81[ASN][1000 genomes]
rs7995946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7998770	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9316563	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9526819	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9526821	0.84[ASN][1000 genomes]
rs9526823	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9526825	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9526832	0.89[ASN][1000 genomes]
rs9526837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526841	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9526842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535812	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs9535822	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9535825	0.80[CHB][hapmap]
rs9535826	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9535829	0.84[ASN][1000 genomes]
rs9535832	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535833	0.85[ASN][1000 genomes]
rs9535836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs9535849	0.91[ASN][1000 genomes]
rs9535851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9535856	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9535858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs9535860	0.96[ASN][1000 genomes]
rs9535861	0.81[CHB][hapmap]
rs9535862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9535866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9535867	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535872	0.99[ASN][1000 genomes]
rs9535873	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535883	0.85[EUR][1000 genomes]
rs9535885	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563084	0.86[ASN][1000 genomes]
rs9563089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs9563091	0.93[ASN][1000 genomes]
rs9563093	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568682	0.80[CHB][hapmap]
rs9568684	0.83[JPT][hapmap]
rs9568693	0.91[ASN][1000 genomes]
rs9568695	0.92[ASN][1000 genomes]
rs9568708	0.93[ASN][1000 genomes]
rs9568713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[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	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	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
4	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
5	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
6	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
7	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535879	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9535879	CKAP2	cis	Nerve Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703400-52705400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:52703600-52704800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr13:52703600-52705000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:52703600-52705000	Weak transcription	Brain Germinal Matrix	brain
5	chr13:52703600-52705000	Weak transcription	A549	lung
6	chr13:52703600-52705000	Weak transcription	HepG2	liver
7	chr13:52703600-52705200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:52703600-52705200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:52703600-52705200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:52703600-52705200	Weak transcription	Liver	Liver
11	chr13:52703600-52705200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:52703600-52705200	Weak transcription	Brain Substantia Nigra	brain
13	chr13:52703600-52705200	Weak transcription	Left Ventricle	heart
14	chr13:52703600-52705200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:52703600-52705400	Weak transcription	NH-A	brain
16	chr13:52703600-52705600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:52703600-52705600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:52703600-52705600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:52703600-52705800	Weak transcription	Lung	lung
20	chr13:52703600-52705800	Weak transcription	NHDF-Ad	bronchial
21	chr13:52703600-52706000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr13:52703600-52706000	Weak transcription	Aorta	Aorta
23	chr13:52703600-52706400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr13:52703600-52706400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:52703600-52707000	Weak transcription	Thymus	Thymus
26	chr13:52703600-52709600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr13:52703600-52720400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr13:52703600-52725200	Weak transcription	Right Ventricle	heart
29	chr13:52703600-52725200	Weak transcription	Small Intestine	intestine
30	chr13:52703600-52725600	Weak transcription	Fetal Brain Male	brain
31	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
32	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
33	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
35	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
36	chr13:52703800-52704800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr13:52703800-52704800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:52703800-52704800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr13:52703800-52704800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr13:52703800-52705000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:52703800-52705000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr13:52703800-52705000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:52703800-52705200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr13:52703800-52705200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr13:52703800-52705200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:52703800-52705200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr13:52703800-52705200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr13:52703800-52705200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:52703800-52705200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr13:52703800-52705200	Weak transcription	Adipose Nuclei	Adipose

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