Variant report

Variant	rs227627
Chromosome Location	chr20:24912107-24912108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24910467..24912747-chr20:24972358..24974415,2	MCF-7	breast:
2	chr20:24909343..24912693-chr20:24913170..24916017,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C20orf3-1	chr20:24911284-24912866	ENSG00000250527

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1056033	0.91[ASN][1000 genomes]
rs1056036	0.88[ASN][1000 genomes]
rs11700073	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11905625	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11906373	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12625319	0.89[ASN][1000 genomes]
rs13041643	0.91[ASN][1000 genomes]
rs1331286	0.86[ASN][1000 genomes]
rs1535042	0.90[ASN][1000 genomes]
rs1854849	0.86[ASN][1000 genomes]
rs1977540	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2008275	0.86[ASN][1000 genomes]
rs2092565	0.91[ASN][1000 genomes]
rs2103736	0.91[ASN][1000 genomes]
rs2151462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2151463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179729	0.91[ASN][1000 genomes]
rs2179730	0.88[ASN][1000 genomes]
rs2206891	0.82[ASN][1000 genomes]
rs2225459	0.91[ASN][1000 genomes]
rs2235847	0.86[ASN][1000 genomes]
rs227590	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs227597	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs227598	0.83[ASN][1000 genomes]
rs227608	0.83[AMR][1000 genomes]
rs227609	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227612	0.89[AMR][1000 genomes]
rs227613	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs227614	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227615	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227618	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227619	0.95[ASN][1000 genomes]
rs227620	0.95[ASN][1000 genomes]
rs227621	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227622	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227623	0.95[ASN][1000 genomes]
rs227624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227626	0.95[ASN][1000 genomes]
rs227628	0.95[ASN][1000 genomes]
rs227629	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227630	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227631	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227632	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227633	0.95[ASN][1000 genomes]
rs227634	0.95[ASN][1000 genomes]
rs227635	0.95[ASN][1000 genomes]
rs227639	0.95[ASN][1000 genomes]
rs227643	0.95[ASN][1000 genomes]
rs227646	0.95[ASN][1000 genomes]
rs227648	0.95[ASN][1000 genomes]
rs227649	0.85[ASN][1000 genomes]
rs227650	0.95[ASN][1000 genomes]
rs227651	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227652	0.95[ASN][1000 genomes]
rs227653	0.95[ASN][1000 genomes]
rs227657	0.95[ASN][1000 genomes]
rs227658	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227659	0.95[ASN][1000 genomes]
rs2387362	0.81[AMR][1000 genomes]
rs2387365	0.86[ASN][1000 genomes]
rs2387366	0.91[ASN][1000 genomes]
rs2387572	0.91[ASN][1000 genomes]
rs2424691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2892279	0.88[ASN][1000 genomes]
rs34419834	0.91[ASN][1000 genomes]
rs4273288	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4462848	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4527284	0.85[ASN][1000 genomes]
rs4539860	0.90[ASN][1000 genomes]
rs45468392	0.95[ASN][1000 genomes]
rs45556041	0.95[ASN][1000 genomes]
rs4594518	0.82[ASN][1000 genomes]
rs4813541	0.91[ASN][1000 genomes]
rs4813542	0.91[ASN][1000 genomes]
rs4815325	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4815327	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4815337	0.91[ASN][1000 genomes]
rs4815339	0.89[ASN][1000 genomes]
rs4815340	0.91[ASN][1000 genomes]
rs4815341	0.88[ASN][1000 genomes]
rs4815351	0.87[ASN][1000 genomes]
rs4815355	0.91[ASN][1000 genomes]
rs4815357	0.86[ASN][1000 genomes]
rs56312312	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57265446	0.88[ASN][1000 genomes]
rs58244398	0.90[ASN][1000 genomes]
rs6036976	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6050131	0.81[ASN][1000 genomes]
rs6050134	0.86[ASN][1000 genomes]
rs6050177	0.88[ASN][1000 genomes]
rs6050179	0.88[ASN][1000 genomes]
rs6050181	0.88[ASN][1000 genomes]
rs6050201	0.88[ASN][1000 genomes]
rs6083684	0.91[ASN][1000 genomes]
rs6083685	0.91[ASN][1000 genomes]
rs6083686	0.91[ASN][1000 genomes]
rs6083688	0.91[ASN][1000 genomes]
rs6083692	0.89[ASN][1000 genomes]
rs6083699	0.91[ASN][1000 genomes]
rs6083709	0.86[ASN][1000 genomes]
rs6106975	0.88[ASN][1000 genomes]
rs6106984	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114980	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114981	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114984	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114988	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132773	0.91[ASN][1000 genomes]
rs6132774	0.91[ASN][1000 genomes]
rs6132775	0.95[ASN][1000 genomes]
rs6132777	0.95[ASN][1000 genomes]
rs6132778	0.95[ASN][1000 genomes]
rs6132783	0.84[ASN][1000 genomes]
rs6138406	0.82[ASN][1000 genomes]
rs6138407	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6138408	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6138409	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6138417	0.91[ASN][1000 genomes]
rs6138423	0.91[ASN][1000 genomes]
rs6138431	0.85[ASN][1000 genomes]
rs6138435	0.91[ASN][1000 genomes]
rs6138437	0.91[ASN][1000 genomes]
rs6138438	0.95[ASN][1000 genomes]
rs6138442	0.90[ASN][1000 genomes]
rs6138453	0.86[ASN][1000 genomes]
rs6138455	0.90[ASN][1000 genomes]
rs6138456	0.90[ASN][1000 genomes]
rs6138457	0.90[ASN][1000 genomes]
rs6138458	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138460	0.84[ASN][1000 genomes]
rs6138461	0.80[ASN][1000 genomes]
rs62215110	0.95[ASN][1000 genomes]
rs62215115	0.95[ASN][1000 genomes]
rs62215128	0.90[ASN][1000 genomes]
rs62215131	0.90[ASN][1000 genomes]
rs6707	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7268095	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7269416	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs735886	0.91[ASN][1000 genomes]
rs8125909	0.90[ASN][1000 genomes]
rs8183891	0.86[ASN][1000 genomes]
rs914314	0.86[ASN][1000 genomes]
rs926661	0.88[ASN][1000 genomes]
rs926662	0.91[ASN][1000 genomes]
rs9753592	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv432115	chr20:24871385-24915839	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058559	chr20:24880415-24923818	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1061536	chr20:24880777-24930642	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1060158	chr20:24887819-24918081	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1066090	chr20:24887819-24923818	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1065568	chr20:24887819-24925706	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	4 gene(s)	inside rSNPs	diseases
12	nsv524921	chr20:24897355-24932028	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv964444	chr20:24899460-24934649	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	esv2752899	chr20:24899800-24923800	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24901400-24915200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:24908600-24912400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:24909600-24913400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:24910400-24913200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:24910600-24912200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:24910600-24913000	Enhancers	Fetal Thymus	thymus
7	chr20:24910800-24912400	Enhancers	Adipose Nuclei	Adipose
8	chr20:24911000-24912200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr20:24911000-24912200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr20:24911000-24913400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr20:24911000-24914600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr20:24911000-24914600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr20:24911000-24914600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr20:24911000-24915200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr20:24911200-24912200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr20:24911200-24912200	Active TSS	Primary B cells from cord blood	blood
17	chr20:24911200-24912200	Active TSS	Gastric	stomach
18	chr20:24911200-24913000	Enhancers	HSMMtube	muscle
19	chr20:24911200-24913600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr20:24911200-24914000	Weak transcription	Fetal Intestine Small	intestine
21	chr20:24911400-24912200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr20:24911400-24913400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr20:24911400-24913800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr20:24911400-24915800	Enhancers	Thymus	Thymus
25	chr20:24911600-24912400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr20:24911600-24912400	Enhancers	Colonic Mucosa	Colon
27	chr20:24911800-24912600	Enhancers	Duodenum Mucosa	Duodenum
28	chr20:24911800-24913000	Enhancers	HMEC	breast
29	chr20:24911800-24913000	Enhancers	NHEK	skin
30	chr20:24911800-24913200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:24911800-24913400	Enhancers	Primary T cells from cord blood	blood
32	chr20:24911800-24913400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr20:24911800-24913400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr20:24911800-24913800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr20:24911800-24913800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr20:24911800-24913800	Weak transcription	Fetal Intestine Large	intestine
37	chr20:24911800-24914200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:24911800-24914600	Enhancers	Placenta	Placenta
39	chr20:24912000-24912200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr20:24912000-24912200	Enhancers	Esophagus	oesophagus
41	chr20:24912000-24912200	Enhancers	Fetal Kidney	kidney
42	chr20:24912000-24912200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr20:24912000-24912200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr20:24912000-24912200	Flanking Active TSS	Stomach Mucosa	stomach
45	chr20:24912000-24912200	Enhancers	A549	lung
46	chr20:24912000-24912400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr20:24912000-24912400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr20:24912000-24912400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr20:24912000-24912400	Flanking Active TSS	Pancreas	Pancrea
50	chr20:24912000-24912600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links