Variant report

Variant	rs9535880
Chromosome Location	chr13:52706143-52706144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52376747..52380251-chr13:52704508..52706445,3	MCF-7	breast:

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
ENSG00000102796	Chromatin interaction
ENSG00000231856	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1004576	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1055062	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1060631	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11616964	0.85[ASN][1000 genomes]
rs11620583	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs12146904	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12431310	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12584961	0.85[ASN][1000 genomes]
rs1571189	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs1801243	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1886538	0.81[CHB][hapmap]
rs1886542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886543	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886544	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886547	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs1924611	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1998696	0.91[ASN][1000 genomes]
rs2004866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs2181891	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2274202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277448	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2296347	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2296348	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296350	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2408549	0.94[ASN][1000 genomes]
rs2408550	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs2408551	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs2408552	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2408554	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408611	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393037	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897964	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897976	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897977	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35895576	0.87[ASN][1000 genomes]
rs3742289	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3783242	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3818422	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3825528	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[ASN][1000 genomes]
rs4297592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4497567	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4941727	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs55772266	0.94[ASN][1000 genomes]
rs61958812	0.94[ASN][1000 genomes]
rs6561656	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6561658	0.89[CEU][hapmap]
rs6650383	0.90[ASN][1000 genomes]
rs66849828	0.82[EUR][1000 genomes]
rs723102	0.93[ASN][1000 genomes]
rs723103	0.93[ASN][1000 genomes]
rs732071	0.81[CHB][hapmap]
rs7320831	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7321120	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7321435	0.81[CHB][hapmap]
rs7324458	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7327634	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs7337430	0.87[ASN][1000 genomes]
rs747781	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs755363	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.97[ASN][1000 genomes]
rs7981904	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7991237	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs7993492	0.81[ASN][1000 genomes]
rs7995946	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs7998770	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9316563	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9526819	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs9526821	0.84[ASN][1000 genomes]
rs9526823	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526825	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526832	0.89[ASN][1000 genomes]
rs9526837	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526841	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535812	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535822	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs9535825	0.81[CHB][hapmap]
rs9535826	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs9535828	0.87[CHD][hapmap]
rs9535829	0.84[ASN][1000 genomes]
rs9535832	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535833	0.85[ASN][1000 genomes]
rs9535836	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs9535849	0.91[ASN][1000 genomes]
rs9535851	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs9535856	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9535858	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9535860	0.96[ASN][1000 genomes]
rs9535861	0.82[CHB][hapmap]
rs9535862	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs9535866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.99[ASN][1000 genomes]
rs9535867	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535872	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535873	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535879	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];0.86[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];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563084	0.86[ASN][1000 genomes]
rs9563089	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[ASN][1000 genomes]
rs9563091	0.93[ASN][1000 genomes]
rs9563093	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568682	0.81[CHB][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[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9535880	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9535880	CKAP2	cis	cerebellum	SCAN
rs9535880	CKAP2	cis	parietal	SCAN
rs9535880	NEK3	cis	cerebellum	SCAN
rs9535880	CKAP2	cis	Artery Tibial	GTEx
rs9535880	CKAP2	cis	Nerve Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703600-52706400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:52703600-52706400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:52703600-52707000	Weak transcription	Thymus	Thymus
4	chr13:52703600-52709600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr13:52703600-52720400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr13:52703600-52725200	Weak transcription	Right Ventricle	heart
7	chr13:52703600-52725200	Weak transcription	Small Intestine	intestine
8	chr13:52703600-52725600	Weak transcription	Fetal Brain Male	brain
9	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
10	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
11	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
13	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
14	chr13:52703800-52706400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr13:52703800-52706400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr13:52703800-52707000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr13:52703800-52707000	Weak transcription	Fetal Kidney	kidney
18	chr13:52703800-52709000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr13:52703800-52720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr13:52703800-52720400	Weak transcription	HSMM	muscle
21	chr13:52703800-52723800	Weak transcription	Colonic Mucosa	Colon
22	chr13:52703800-52724800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr13:52703800-52731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:52703800-52731400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:52703800-52731400	Weak transcription	Spleen	Spleen
26	chr13:52703800-52732600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr13:52703800-52732600	Weak transcription	HMEC	breast
28	chr13:52703800-52733200	Weak transcription	Gastric	stomach
29	chr13:52704000-52707000	Weak transcription	Colon Smooth Muscle	Colon
30	chr13:52704000-52711000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
32	chr13:52704200-52706200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr13:52704200-52708800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr13:52704200-52709600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr13:52704200-52709600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr13:52704200-52725400	Weak transcription	Primary T cells from cord blood	blood
37	chr13:52704600-52707400	Strong transcription	Fetal Heart	heart
38	chr13:52704800-52708000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:52704800-52710400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:52704800-52727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:52704800-52730000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr13:52705000-52707800	Strong transcription	A549	lung
43	chr13:52705000-52708400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:52705000-52710400	Strong transcription	Brain Germinal Matrix	brain
45	chr13:52705000-52711000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:52705000-52711200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:52705000-52712400	Strong transcription	HepG2	liver
48	chr13:52705000-52716200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr13:52705200-52706200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr13:52705200-52706600	Strong transcription	Brain Cingulate Gyrus	brain

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