Variant report

Variant	rs6138455
Chromosome Location	chr20:24972799-24972800
allele	C/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:24972188..24974753-chr20:24992355..24994002,2	K562	blood:
2	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:
3	chr20:24972013..24974485-chr20:25388171..25390084,2	MCF-7	breast:
4	chr20:24971936..24974944-chr20:25175039..25178381,3	MCF-7	breast:
5	chr20:24972575..24975462-chr20:25603621..25605250,2	K562	blood:
6	chr20:24972059..24974449-chr20:25176101..25177683,2	MCF-7	breast:
7	chr20:24971946..24973582-chr20:25227704..25229248,2	MCF-7	breast:
8	chr20:24971839..24974533-chr20:25228512..25230139,2	MCF-7	breast:
9	chr20:24972184..24974531-chr20:25057258..25059368,3	MCF-7	breast:
10	chr1:151227020..151227760-chr20:24972743..24973473,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000170191	Chromatin interaction
ENSG00000100987	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000197586	Chromatin interaction
ENSG00000100994	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000154930	Chromatin interaction
ENSG00000101003	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056033	0.86[ASN][1000 genomes]
rs1056036	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11700073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11905625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11906373	0.93[ASN][1000 genomes]
rs12625319	0.84[ASN][1000 genomes]
rs13041643	0.86[ASN][1000 genomes]
rs1331286	0.85[ASN][1000 genomes]
rs1535042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854849	0.85[ASN][1000 genomes]
rs1977540	0.83[ASN][1000 genomes]
rs2008275	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2092565	0.86[ASN][1000 genomes]
rs2103736	0.86[ASN][1000 genomes]
rs2151462	0.93[ASN][1000 genomes]
rs2151463	0.93[ASN][1000 genomes]
rs2179729	0.86[ASN][1000 genomes]
rs2179730	0.88[ASN][1000 genomes]
rs2179732	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2206891	0.82[ASN][1000 genomes]
rs2225459	0.86[ASN][1000 genomes]
rs2235847	0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs227590	0.82[ASN][1000 genomes]
rs227598	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs227613	0.87[ASN][1000 genomes]
rs227614	0.90[ASN][1000 genomes]
rs227615	0.86[ASN][1000 genomes]
rs227616	0.93[ASN][1000 genomes]
rs227618	0.85[ASN][1000 genomes]
rs227619	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227620	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227621	0.93[ASN][1000 genomes]
rs227622	0.93[ASN][1000 genomes]
rs227623	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227624	0.93[ASN][1000 genomes]
rs227625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227626	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227627	0.90[ASN][1000 genomes]
rs227628	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227629	0.93[ASN][1000 genomes]
rs227630	0.93[ASN][1000 genomes]
rs227631	0.93[ASN][1000 genomes]
rs227632	0.93[ASN][1000 genomes]
rs227633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227635	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227639	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227643	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227646	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227648	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227649	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs227650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227651	0.93[ASN][1000 genomes]
rs227652	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227657	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227658	0.93[ASN][1000 genomes]
rs227659	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2387365	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2387366	0.86[ASN][1000 genomes]
rs2387572	0.86[ASN][1000 genomes]
rs2424691	0.93[ASN][1000 genomes]
rs2892279	0.88[ASN][1000 genomes]
rs34419834	0.86[ASN][1000 genomes]
rs3746330	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4273288	0.83[ASN][1000 genomes]
rs4527284	0.80[ASN][1000 genomes]
rs4539860	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45468392	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45556041	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813541	0.86[ASN][1000 genomes]
rs4813542	0.86[ASN][1000 genomes]
rs4815327	0.83[ASN][1000 genomes]
rs4815337	0.86[ASN][1000 genomes]
rs4815339	0.84[ASN][1000 genomes]
rs4815340	0.86[ASN][1000 genomes]
rs4815341	0.88[ASN][1000 genomes]
rs4815351	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4815355	0.86[ASN][1000 genomes]
rs4815357	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs56312312	0.97[ASN][1000 genomes]
rs57265446	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58244398	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036976	0.83[ASN][1000 genomes]
rs6050118	0.80[AMR][1000 genomes]
rs6050131	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050134	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6050177	0.88[ASN][1000 genomes]
rs6050179	0.88[ASN][1000 genomes]
rs6050181	0.88[ASN][1000 genomes]
rs6050198	0.85[CHB][hapmap]
rs6050201	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6050249	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6050255	0.86[JPT][hapmap]
rs6050259	0.86[JPT][hapmap]
rs6050261	0.86[JPT][hapmap]
rs6083684	0.86[ASN][1000 genomes]
rs6083685	0.86[ASN][1000 genomes]
rs6083686	0.86[ASN][1000 genomes]
rs6083688	0.86[ASN][1000 genomes]
rs6083692	0.84[ASN][1000 genomes]
rs6083699	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6083709	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6106975	0.88[ASN][1000 genomes]
rs6106984	0.97[ASN][1000 genomes]
rs6114980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6114981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6114984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6114988	0.97[ASN][1000 genomes]
rs6132773	0.86[ASN][1000 genomes]
rs6132774	0.86[ASN][1000 genomes]
rs6132775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132783	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132784	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs6132789	0.86[JPT][hapmap]
rs6138417	0.86[ASN][1000 genomes]
rs6138423	0.86[ASN][1000 genomes]
rs6138431	0.80[ASN][1000 genomes]
rs6138435	0.86[ASN][1000 genomes]
rs6138437	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6138438	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138456	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138460	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138461	0.85[ASN][1000 genomes]
rs6138463	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138465	0.81[ASN][1000 genomes]
rs6138466	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138473	0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.86[JPT][hapmap]
rs62215110	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62215115	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62215128	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215131	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7268095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7269416	0.97[ASN][1000 genomes]
rs735886	0.86[ASN][1000 genomes]
rs8125909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8183891	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs914314	0.85[ASN][1000 genomes]
rs926661	0.88[ASN][1000 genomes]
rs926662	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
6	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6138455	CST7	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24971000-24972800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr20:24971000-24972800	Flanking Active TSS	Dnd41	blood
3	chr20:24971000-24973200	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr20:24971000-24974200	Active TSS	Right Atrium	heart
5	chr20:24971200-24973600	Active TSS	Liver	Liver
6	chr20:24971400-24972800	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr20:24971400-24973000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr20:24971600-24972800	Flanking Active TSS	Hela-S3	cervix
9	chr20:24971600-24973000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr20:24971600-24973200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr20:24971600-24973200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:24971600-24973200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr20:24971800-24972800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr20:24971800-24972800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr20:24971800-24972800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr20:24971800-24972800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr20:24971800-24972800	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr20:24971800-24972800	Flanking Active TSS	Fetal Brain Female	brain
19	chr20:24971800-24972800	Flanking Active TSS	HMEC	breast
20	chr20:24971800-24973000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr20:24971800-24973000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr20:24971800-24973800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr20:24971800-24974000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr20:24972000-24972800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr20:24972000-24972800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr20:24972000-24973000	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr20:24972000-24973000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr20:24972000-24973000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr20:24972000-24973000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:24972000-24973000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr20:24972000-24973000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr20:24972000-24973800	Active TSS	NHLF	lung
33	chr20:24972000-24974000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr20:24972000-24974400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr20:24972200-24972800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr20:24972200-24972800	Flanking Active TSS	NH-A	brain
37	chr20:24972200-24973000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:24972200-24973200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr20:24972200-24973600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr20:24972200-24974000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr20:24972200-24974000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr20:24972200-24974000	Active TSS	NHDF-Ad	bronchial
43	chr20:24972400-24972800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:24972400-24972800	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr20:24972400-24972800	Flanking Active TSS	Fetal Stomach	stomach
46	chr20:24972400-24972800	Flanking Active TSS	Fetal Thymus	thymus
47	chr20:24972400-24972800	Flanking Active TSS	Right Ventricle	heart
48	chr20:24972400-24973000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr20:24972400-24973000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr20:24972400-24973000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links