Variant report

Variant	rs2540524
Chromosome Location	chr13:51289148-51289149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-4	chr13:51287754-51289476	NONHSAT033865

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1323886	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs1853558	0.85[EUR][1000 genomes]
rs1853559	0.85[EUR][1000 genomes]
rs2476624	0.82[YRI][hapmap]
rs2492345	0.82[EUR][1000 genomes]
rs2540523	0.86[EUR][1000 genomes]
rs2706228	0.85[EUR][1000 genomes]
rs2706229	0.87[EUR][1000 genomes]
rs2706235	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs2706241	0.85[EUR][1000 genomes]
rs2706242	0.80[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2706244	0.85[EUR][1000 genomes]
rs2761841	0.85[EUR][1000 genomes]
rs2761842	0.86[EUR][1000 genomes]
rs2761843	0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs2761844	0.85[EUR][1000 genomes]
rs2761845	0.85[EUR][1000 genomes]
rs2761846	0.85[EUR][1000 genomes]
rs2761849	0.82[EUR][1000 genomes]
rs2761850	0.82[EUR][1000 genomes]
rs2761851	0.82[EUR][1000 genomes]
rs2761852	0.82[EUR][1000 genomes]
rs2761854	0.82[EUR][1000 genomes]
rs2812235	0.85[EUR][1000 genomes]
rs2812242	0.82[EUR][1000 genomes]
rs2812243	0.82[EUR][1000 genomes]
rs2812246	0.82[EUR][1000 genomes]
rs2812247	0.82[EUR][1000 genomes]
rs2812249	0.82[EUR][1000 genomes]
rs2812250	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
2	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1037350	chr13:51272518-51447354	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv561643	chr13:51286083-51306330	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51269400-51296800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:51285000-51289400	Enhancers	Fetal Muscle Leg	muscle
3	chr13:51285000-51290000	Weak transcription	Brain Substantia Nigra	brain
4	chr13:51286200-51290600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr13:51287200-51289200	Enhancers	Fetal Thymus	thymus
6	chr13:51287600-51289600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr13:51287600-51290800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr13:51287800-51289200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:51287800-51289200	Enhancers	HMEC	breast
10	chr13:51287800-51289800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr13:51287800-51290600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr13:51287800-51292000	Active TSS	Brain Hippocampus Middle	brain
13	chr13:51288400-51289200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr13:51288400-51289200	Enhancers	Duodenum Mucosa	Duodenum
15	chr13:51288400-51289400	Enhancers	Adipose Nuclei	Adipose
16	chr13:51288400-51290600	Enhancers	Primary B cells from peripheral blood	blood
17	chr13:51288400-51291600	Weak transcription	HepG2	liver
18	chr13:51288600-51289200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr13:51288600-51289400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr13:51288600-51289800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:51288600-51290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr13:51288600-51290200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr13:51288600-51290400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr13:51288600-51290600	Enhancers	Dnd41	blood
25	chr13:51288600-51291600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:51289000-51289200	Enhancers	Primary hematopoietic stem cells	blood
27	chr13:51289000-51289200	Enhancers	Placenta	Placenta
28	chr13:51289000-51289400	Enhancers	Primary T cells from cord blood	blood
29	chr13:51289000-51290200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr13:51289000-51290600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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