Variant report

Variant	rs17083228
Chromosome Location	chr5:92906447-92906448
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR2F1-1	chr5:92906435-92907480	XLOC_004475
2	lnc-FAM172A-2	chr5:92906204-92907441	NONHSAT102809
3	lnc-FAM172A-2	chr5:92906204-92907049	NR_109825
4	lnc-FAM172A-2	chr5:92906204-92906525	ENSG00000237187.4
5	lnc-FAM172A-2	chr5:92905596-92907049	ENSG00000237187.4
6	lnc-FAM172A-2	chr5:92905596-92906499	ENSG00000237187.4
7	lnc-NR2F1-1	chr5:92905603-92907480	NONHSAT102810
8	lnc-FAM172A-2	chr5:92906204-92906525	NONHSAT102787

No data

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10041792	0.86[JPT][hapmap]
rs1004941	0.86[JPT][hapmap]
rs10050364	0.85[JPT][hapmap]
rs10051878	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10060331	0.86[JPT][hapmap]
rs10067541	0.86[JPT][hapmap]
rs10071040	0.86[JPT][hapmap]
rs1038686	0.86[JPT][hapmap]
rs1046217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10476520	0.86[JPT][hapmap]
rs10514376	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11135388	0.89[EUR][1000 genomes]
rs11951859	0.85[EUR][1000 genomes]
rs11952115	0.91[EUR][1000 genomes]
rs11952600	0.88[EUR][1000 genomes]
rs11960608	0.91[EUR][1000 genomes]
rs12186735	0.93[ASN][1000 genomes]
rs12187239	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188716	0.93[ASN][1000 genomes]
rs12188845	0.88[EUR][1000 genomes]
rs12188905	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13154650	0.86[JPT][hapmap]
rs13161885	0.86[JPT][hapmap]
rs1370977	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457101	0.89[EUR][1000 genomes]
rs17082127	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17082129	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17083145	0.85[EUR][1000 genomes]
rs17083155	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17083181	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17083191	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083194	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083198	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083200	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083213	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17083297	0.86[JPT][hapmap]
rs17312456	0.86[JPT][hapmap]
rs17370695	0.93[ASN][1000 genomes]
rs1824153	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1844343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083227	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279473	0.93[ASN][1000 genomes]
rs2344387	0.88[EUR][1000 genomes]
rs3776601	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs55861967	0.85[EUR][1000 genomes]
rs57165666	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57690257	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59360932	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61324921	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61352323	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556823	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6556824	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556826	0.80[EUR][1000 genomes]
rs6556829	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6866771	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877616	0.86[JPT][hapmap]
rs6879816	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880843	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6881815	0.86[JPT][hapmap]
rs6884138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6889857	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890998	0.86[JPT][hapmap]
rs6895356	0.86[JPT][hapmap]
rs6898507	0.86[JPT][hapmap]
rs73133214	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133217	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133226	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133228	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73133239	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73133251	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133254	0.85[EUR][1000 genomes]
rs73133258	0.88[EUR][1000 genomes]
rs73133261	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133265	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133275	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133278	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133280	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133282	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133283	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133287	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133289	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133292	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133301	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135313	0.92[EUR][1000 genomes]
rs73135320	0.93[ASN][1000 genomes]
rs73135321	0.93[ASN][1000 genomes]
rs73772907	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702348	0.86[JPT][hapmap]
rs7702649	0.86[JPT][hapmap]
rs7712388	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7712899	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715034	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7717718	0.86[JPT][hapmap]
rs7721168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7721509	1.00[CHB][hapmap]
rs7727107	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736624	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9314086	0.86[JPT][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	nsv1022355	chr5:92846496-92911797	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
2	nsv537807	chr5:92846496-92911797	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
3	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv1819334	chr5:92892591-92956733	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv882383	chr5:92895401-92928346	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv823130	chr5:92896346-92966016	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv4918	chr5:92898426-92943359	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv823132	chr5:92898512-92969668	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92860000-92908000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:92889600-92909800	Weak transcription	Ovary	ovary
3	chr5:92900600-92908200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:92900800-92914400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:92901000-92907200	Weak transcription	Osteobl	bone
6	chr5:92901000-92908000	Weak transcription	NH-A	brain
7	chr5:92903600-92907200	Weak transcription	Fetal Kidney	kidney
8	chr5:92904800-92907000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:92905400-92907600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:92905400-92910200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:92905600-92906600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr5:92905600-92906600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:92905600-92907000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr5:92905600-92907200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr5:92905600-92907600	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr5:92905600-92908800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr5:92905600-92908800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:92905600-92909400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr5:92905600-92909600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:92905600-92909600	ZNF genes & repeats	Placenta	Placenta
21	chr5:92905800-92907000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:92905800-92907000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
23	chr5:92905800-92907600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr5:92905800-92909600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:92906000-92906600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:92906000-92906600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
27	chr5:92906000-92906600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
28	chr5:92906000-92906600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
29	chr5:92906000-92906600	Bivalent/Poised TSS	Colonic Mucosa	Colon
30	chr5:92906000-92906600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr5:92906000-92906600	Bivalent Enhancer	Left Ventricle	heart
32	chr5:92906000-92906800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:92906000-92906800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr5:92906000-92906800	Bivalent Enhancer	Fetal Heart	heart
35	chr5:92906000-92906800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr5:92906000-92906800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
37	chr5:92906000-92907000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr5:92906000-92907000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr5:92906000-92907000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:92906000-92907000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr5:92906000-92907200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr5:92906000-92907200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr5:92906000-92907200	Bivalent Enhancer	Lung	lung
44	chr5:92906000-92907800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:92906000-92909000	Bivalent Enhancer	Spleen	Spleen
46	chr5:92906000-92909200	Enhancers	Pancreas	Pancrea
47	chr5:92906000-92911200	Bivalent Enhancer	Fetal Brain Male	brain
48	chr5:92906200-92906600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
49	chr5:92906200-92906600	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:92906200-92906600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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