Variant report

Variant	rs168833
Chromosome Location	chr5:115643398-115643399
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-4	chr5:115643332-115643482	NONHSAT103359

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10042163	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10055039	1.00[YRI][hapmap]
rs1090076	1.00[JPT][hapmap]
rs11241386	0.82[ASN][1000 genomes]
rs11957456	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs12653124	0.90[CEU][hapmap];0.83[YRI][hapmap]
rs1351136	0.82[ASN][1000 genomes]
rs1351137	0.82[ASN][1000 genomes]
rs1396480	1.00[YRI][hapmap]
rs1508874	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs153578	0.85[ASN][1000 genomes]
rs153591	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153592	0.85[ASN][1000 genomes]
rs153612	0.84[ASN][1000 genomes]
rs153614	0.90[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs187591	0.84[ASN][1000 genomes]
rs194182	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs2136206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs253953	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs253956	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs253960	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs253967	0.80[EUR][1000 genomes]
rs254149	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs254154	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27499	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27500	0.82[ASN][1000 genomes]
rs28083	0.85[ASN][1000 genomes]
rs28125	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs37182	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs4463206	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap]
rs4920906	1.00[YRI][hapmap]
rs6594955	1.00[YRI][hapmap]
rs6860795	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6878279	1.00[YRI][hapmap]
rs6896229	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs712575	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs712580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72808983	0.83[ASN][1000 genomes]
rs784482	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs785368	0.90[CEU][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs804141	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs804142	0.82[ASN][1000 genomes]
rs9285884	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9326992	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1018001	chr5:115640603-115660285	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
4	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
5	chr5:115634200-115643600	Weak transcription	HepG2	liver
6	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:115634400-115645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:115635400-115643600	Strong transcription	Fetal Intestine Large	intestine
9	chr5:115636200-115643600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:115637600-115643400	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:115637600-115643800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:115638400-115643400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:115638400-115644000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:115638800-115643400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:115639000-115644400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:115639400-115645200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr5:115639600-115643600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:115639600-115647400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:115639800-115643400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:115640000-115644200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:115640200-115643600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr5:115640200-115645600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr5:115640200-115647200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr5:115640400-115643400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:115640400-115643400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
26	chr5:115640400-115643600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
27	chr5:115640400-115644400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr5:115640400-115644400	ZNF genes & repeats	Dnd41	blood
29	chr5:115640400-115645800	ZNF genes & repeats	Primary T cells from cord blood	blood
30	chr5:115640600-115643600	ZNF genes & repeats	Ovary	ovary
31	chr5:115640600-115645200	ZNF genes & repeats	Fetal Lung	lung
32	chr5:115640600-115645200	ZNF genes & repeats	Fetal Muscle Leg	muscle
33	chr5:115640600-115645600	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr5:115640800-115643600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
35	chr5:115640800-115643800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:115640800-115645600	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr5:115640800-115658200	Weak transcription	Colonic Mucosa	Colon
38	chr5:115641000-115643600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr5:115641000-115653000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:115641400-115644000	ZNF genes & repeats	Brain Anterior Caudate	brain
41	chr5:115641400-115644400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:115641400-115645600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
43	chr5:115641400-115651800	Weak transcription	Esophagus	oesophagus
44	chr5:115641600-115643800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:115641600-115644000	Strong transcription	HSMM	muscle
46	chr5:115641600-115644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:115641600-115647200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:115641800-115643400	ZNF genes & repeats	Brain Substantia Nigra	brain
49	chr5:115641800-115644000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
50	chr5:115641800-115644600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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