Variant report

Variant	rs6138463
Chromosome Location	chr20:24982491-24982492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24981112..24985006-chr20:25036705..25039291,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11700073	0.85[ASN][1000 genomes]
rs11905625	0.85[ASN][1000 genomes]
rs11906373	0.81[ASN][1000 genomes]
rs1535042	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2151462	0.81[ASN][1000 genomes]
rs2151463	0.81[ASN][1000 genomes]
rs227596	0.81[AMR][1000 genomes]
rs227598	0.81[AMR][1000 genomes]
rs227616	0.81[ASN][1000 genomes]
rs227619	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227620	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227621	0.81[ASN][1000 genomes]
rs227622	0.81[ASN][1000 genomes]
rs227623	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227624	0.81[ASN][1000 genomes]
rs227625	0.81[ASN][1000 genomes]
rs227626	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227628	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227629	0.81[ASN][1000 genomes]
rs227630	0.81[ASN][1000 genomes]
rs227631	0.81[ASN][1000 genomes]
rs227632	0.81[ASN][1000 genomes]
rs227633	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227634	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227635	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227639	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227643	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227646	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227648	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227649	0.81[AMR][1000 genomes]
rs227650	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227651	0.81[ASN][1000 genomes]
rs227652	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227653	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227657	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs227658	0.81[ASN][1000 genomes]
rs227659	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2387365	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2424691	0.81[ASN][1000 genomes]
rs3746330	0.81[ASN][1000 genomes]
rs4539860	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs45468392	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs45556041	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56312312	0.85[ASN][1000 genomes]
rs57265446	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58244398	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6050131	0.80[EUR][1000 genomes]
rs6050134	0.86[AMR][1000 genomes]
rs6050249	0.88[ASN][1000 genomes]
rs6106984	0.85[ASN][1000 genomes]
rs6114980	0.85[ASN][1000 genomes]
rs6114981	0.85[ASN][1000 genomes]
rs6114984	0.85[ASN][1000 genomes]
rs6114988	0.85[ASN][1000 genomes]
rs6114992	0.91[ASN][1000 genomes]
rs6132775	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6132777	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6132778	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6132783	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132784	0.83[ASN][1000 genomes]
rs6132785	0.81[ASN][1000 genomes]
rs6138438	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6138442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138455	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138456	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138457	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138458	0.85[ASN][1000 genomes]
rs6138460	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138461	0.87[ASN][1000 genomes]
rs6138464	0.88[ASN][1000 genomes]
rs6138465	0.83[ASN][1000 genomes]
rs6138466	0.81[ASN][1000 genomes]
rs62215110	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62215115	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62215128	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62215131	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7268095	0.85[ASN][1000 genomes]
rs7269416	0.85[ASN][1000 genomes]
rs8125909	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6138463	CST7	cis	Whole Blood	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24974000-24985800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr20:24974000-24985800	Weak transcription	Thymus	Thymus
3	chr20:24974000-24986400	Weak transcription	Aorta	Aorta
4	chr20:24974200-24985200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr20:24974200-24985800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:24974200-24988200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr20:24974400-24983200	Weak transcription	Primary T cells from cord blood	blood
8	chr20:24974400-24992000	Weak transcription	GM12878-XiMat	blood
9	chr20:24974800-24985800	Weak transcription	Spleen	Spleen
10	chr20:24975800-24983200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr20:24975800-24986400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr20:24976000-24983200	Weak transcription	Primary B cells from cord blood	blood
13	chr20:24976000-24983200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr20:24976000-24983200	Weak transcription	Fetal Lung	lung
15	chr20:24976000-24983400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr20:24976000-24985000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr20:24976000-24985000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr20:24976000-24985800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr20:24976000-24985800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr20:24976000-24986000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr20:24976000-24986000	Weak transcription	Colonic Mucosa	Colon
22	chr20:24976000-24986400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr20:24976000-24986400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr20:24976000-24987600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr20:24976000-24988000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr20:24976000-24999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr20:24976200-24983200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr20:24976200-24985800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr20:24976200-24985800	Weak transcription	Adipose Nuclei	Adipose
30	chr20:24976200-24985800	Weak transcription	Lung	lung
31	chr20:24976200-24986200	Weak transcription	Dnd41	blood
32	chr20:24976800-24983200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr20:24976800-24983200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr20:24976800-24986000	Weak transcription	Brain Germinal Matrix	brain
35	chr20:24977000-24983400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr20:24977000-24983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr20:24977000-24986600	Weak transcription	Fetal Thymus	thymus
38	chr20:24977200-24983200	Weak transcription	Fetal Stomach	stomach
39	chr20:24979000-24987400	Weak transcription	Small Intestine	intestine
40	chr20:24979400-24983400	Weak transcription	Fetal Muscle Leg	muscle
41	chr20:24979400-24986000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr20:24980000-24985800	Weak transcription	Gastric	stomach
43	chr20:24980600-24986200	Weak transcription	Right Atrium	heart
44	chr20:24981200-24985200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr20:24981200-24985800	Weak transcription	Brain Substantia Nigra	brain
46	chr20:24981200-24986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr20:24981200-24986600	Weak transcription	Esophagus	oesophagus
48	chr20:24981400-24983200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr20:24981400-24983200	Weak transcription	Fetal Intestine Large	intestine
50	chr20:24981400-24985200	Weak transcription	Colon Smooth Muscle	Colon

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