Variant report

Variant	rs6132784
Chromosome Location	chr20:24987787-24987788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24971913..24973506-chr20:24986297..24987833,2	K562	blood:
2	chr20:24986736..24988583-chr20:25057108..25059778,2	MCF-7	breast:
3	chr20:24972921..24974779-chr20:24986301..24988753,2	MCF-7	breast:
4	chr20:24985071..24988869-chr20:24990703..24995644,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100987	Chromatin interaction
ENSG00000154930	Chromatin interaction
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1007881	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1056036	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11700073	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11905625	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1535042	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2008275	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2179732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2235847	0.94[CHD][hapmap];0.86[JPT][hapmap]
rs227619	0.81[ASN][1000 genomes]
rs227620	0.81[ASN][1000 genomes]
rs227623	0.81[ASN][1000 genomes]
rs227625	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs227626	0.81[ASN][1000 genomes]
rs227628	0.81[ASN][1000 genomes]
rs227633	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs227634	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs227635	0.81[ASN][1000 genomes]
rs227639	0.81[ASN][1000 genomes]
rs227643	0.81[ASN][1000 genomes]
rs227646	0.81[ASN][1000 genomes]
rs227648	0.81[ASN][1000 genomes]
rs227650	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs227652	0.81[ASN][1000 genomes]
rs227653	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs227657	0.81[ASN][1000 genomes]
rs227659	0.81[ASN][1000 genomes]
rs3746330	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs41315094	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45468392	0.81[ASN][1000 genomes]
rs45556041	0.81[ASN][1000 genomes]
rs4815351	1.00[JPT][hapmap]
rs4815357	1.00[JPT][hapmap]
rs58244398	0.81[ASN][1000 genomes]
rs6050201	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6050249	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050255	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050259	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050261	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6083699	1.00[JPT][hapmap]
rs6083709	1.00[JPT][hapmap]
rs60849220	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6114980	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6114981	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6114984	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132775	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6132777	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6132778	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6132783	0.88[ASN][1000 genomes]
rs6132785	0.98[ASN][1000 genomes]
rs6132788	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6132789	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6132790	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6138437	1.00[JPT][hapmap]
rs6138438	0.81[ASN][1000 genomes]
rs6138442	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6138453	1.00[JPT][hapmap]
rs6138455	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs6138456	0.81[ASN][1000 genomes]
rs6138457	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6138458	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6138460	0.88[ASN][1000 genomes]
rs6138461	0.80[ASN][1000 genomes]
rs6138463	0.83[ASN][1000 genomes]
rs6138464	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138465	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138466	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6138473	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6138474	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6138475	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62215110	0.81[ASN][1000 genomes]
rs62215115	0.81[ASN][1000 genomes]
rs62215128	0.81[ASN][1000 genomes]
rs62215131	0.81[ASN][1000 genomes]
rs62217173	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62217174	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62217175	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6707	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7268095	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8125909	0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs8183891	1.00[JPT][hapmap]

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	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
6	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6132784	PLK1S1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24974200-24988200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr20:24974400-24992000	Weak transcription	GM12878-XiMat	blood
3	chr20:24976000-24988000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr20:24976000-24999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr20:24981600-24989600	Weak transcription	Brain Angular Gyrus	brain
6	chr20:24981600-25003600	Weak transcription	Fetal Heart	heart
7	chr20:24981800-24987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:24981800-24988200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr20:24981800-24989800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:24981800-24992600	Weak transcription	Psoas Muscle	Psoas
11	chr20:24981800-24992800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:24981800-24997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr20:24983200-24990000	Strong transcription	Fetal Lung	lung
14	chr20:24983200-24996800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr20:24983200-25003800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr20:24983200-25005000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr20:24983200-25007800	Strong transcription	Primary T cells from cord blood	blood
18	chr20:24983200-25008200	Strong transcription	Primary B cells from cord blood	blood
19	chr20:24983400-24995400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr20:24983400-24996600	Strong transcription	Placenta	Placenta
21	chr20:24983800-24994800	Strong transcription	Primary hematopoietic stem cells	blood
22	chr20:24983800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr20:24984400-24989800	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr20:24984600-24997200	Strong transcription	Fetal Intestine Large	intestine
25	chr20:24985000-24997200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr20:24985000-24997600	Strong transcription	Fetal Intestine Small	intestine
27	chr20:24985000-25004400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr20:24985000-25005600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr20:24985200-24995800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr20:24985200-25002600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr20:24985200-25003200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr20:24985200-25007800	Strong transcription	Fetal Muscle Leg	muscle
33	chr20:24985600-24996600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr20:24985800-24995800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr20:24985800-24997200	Strong transcription	Lung	lung
36	chr20:24985800-24997600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr20:24985800-25002400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr20:24985800-25004200	Strong transcription	Thymus	Thymus
39	chr20:24985800-25004400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr20:24985800-25005000	Strong transcription	Adipose Nuclei	Adipose
41	chr20:24985800-25005800	Strong transcription	Spleen	Spleen
42	chr20:24985800-25006800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr20:24985800-25007600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr20:24985800-25007800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr20:24986000-24988200	Genic enhancers	Rectal Smooth Muscle	rectum
46	chr20:24986000-24990200	Strong transcription	Colonic Mucosa	Colon
47	chr20:24986000-24994800	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr20:24986000-24996200	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr20:24986000-25004800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr20:24986200-24994400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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