Variant report

Variant	rs1886541
Chromosome Location	chr13:52706774-52706775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UTP14C-1	chr13:52706594-52706859	NR_110306
2	lnc-UTP14C-1	chr13:52706594-52706859	NONHSAT033962

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1000892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11839458	0.85[MEX][hapmap];1.00[TSI][hapmap]
rs12870757	0.81[AMR][1000 genomes]
rs17404248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17480245	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17480469	1.00[ASW][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs17482550	1.00[AMR][1000 genomes]
rs17482660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17536694	1.00[ASW][hapmap];0.88[AMR][1000 genomes]
rs1886540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34288155	0.89[AMR][1000 genomes]
rs34326189	0.83[AMR][1000 genomes]
rs35302368	0.81[AMR][1000 genomes]
rs35370885	0.89[AMR][1000 genomes]
rs35703449	0.81[AMR][1000 genomes]
rs4438196	0.81[AMR][1000 genomes]
rs4943053	1.00[ASW][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4943055	1.00[EUR][1000 genomes]
rs4943065	0.85[AMR][1000 genomes]
rs55969405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57604069	0.92[AMR][1000 genomes]
rs59763550	0.85[AMR][1000 genomes]
rs59924615	0.85[AMR][1000 genomes]
rs61247071	0.81[AMR][1000 genomes]
rs71437831	0.81[AMR][1000 genomes]
rs7317742	0.85[AMR][1000 genomes]
rs7320155	0.89[AMR][1000 genomes]
rs7325357	0.85[AMR][1000 genomes]
rs7332381	0.85[AMR][1000 genomes]
rs7334118	0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7338832	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73500202	0.92[AMR][1000 genomes]
rs73502304	0.92[AMR][1000 genomes]
rs73502323	0.85[AMR][1000 genomes]
rs7400215	0.85[AMR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703600-52707000	Weak transcription	Thymus	Thymus
2	chr13:52703600-52709600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr13:52703600-52720400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr13:52703600-52725200	Weak transcription	Right Ventricle	heart
5	chr13:52703600-52725200	Weak transcription	Small Intestine	intestine
6	chr13:52703600-52725600	Weak transcription	Fetal Brain Male	brain
7	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
8	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
9	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
11	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
12	chr13:52703800-52707000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr13:52703800-52707000	Weak transcription	Fetal Kidney	kidney
14	chr13:52703800-52709000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:52703800-52720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr13:52703800-52720400	Weak transcription	HSMM	muscle
17	chr13:52703800-52723800	Weak transcription	Colonic Mucosa	Colon
18	chr13:52703800-52724800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr13:52703800-52731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:52703800-52731400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:52703800-52731400	Weak transcription	Spleen	Spleen
22	chr13:52703800-52732600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr13:52703800-52732600	Weak transcription	HMEC	breast
24	chr13:52703800-52733200	Weak transcription	Gastric	stomach
25	chr13:52704000-52707000	Weak transcription	Colon Smooth Muscle	Colon
26	chr13:52704000-52711000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
28	chr13:52704200-52708800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr13:52704200-52709600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr13:52704200-52709600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:52704200-52725400	Weak transcription	Primary T cells from cord blood	blood
32	chr13:52704600-52707400	Strong transcription	Fetal Heart	heart
33	chr13:52704800-52708000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:52704800-52710400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:52704800-52727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:52704800-52730000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr13:52705000-52707800	Strong transcription	A549	lung
38	chr13:52705000-52708400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr13:52705000-52710400	Strong transcription	Brain Germinal Matrix	brain
40	chr13:52705000-52711000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:52705000-52711200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:52705000-52712400	Strong transcription	HepG2	liver
43	chr13:52705000-52716200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr13:52705200-52707200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr13:52705200-52707800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr13:52705200-52708200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr13:52705200-52708200	Strong transcription	Liver	Liver
48	chr13:52705200-52708400	Strong transcription	Fetal Brain Female	brain
49	chr13:52705200-52708400	Strong transcription	Fetal Lung	lung
50	chr13:52705200-52708400	Strong transcription	HSMMtube	muscle

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