Variant report

Variant	rs6114992
Chromosome Location	chr20:24981120-24981121
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:24981112..24985006-chr20:25036705..25039291,3	MCF-7	breast:
2	chr20:24979571..24981493-chr20:24983135..24984775,2	MCF-7	breast:
3	chr20:24978861..24981333-chr20:24998565..25000190,2	MCF-7	breast:
4	chr20:24980910..24981445-chr20:25046435..25046961,2	MCF-7	breast:
5	chr20:24972646..24975006-chr20:24979195..24981291,2	MCF-7	breast:
6	chr20:24980779..24981584-chr20:25159554..25160358,4	MCF-7	breast:
7	chr20:24971717..24976132-chr20:24977323..24981321,5	K562	blood:
8	chr20:24980657..24981409-chr20:25046140..25046996,4	MCF-7	breast:
9	chr20:24978936..24981881-chr20:25041310..25043065,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction
ENSG00000154930	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1056033	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1056036	0.82[ASN][1000 genomes]
rs11087486	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11699285	0.85[EUR][1000 genomes]
rs11700073	0.82[ASN][1000 genomes]
rs11905625	0.82[ASN][1000 genomes]
rs12625319	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13041643	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008275	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2092565	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2103736	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2179729	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2179730	0.82[ASN][1000 genomes]
rs2225459	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2235847	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2387366	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2387572	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2892279	0.82[ASN][1000 genomes]
rs34419834	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4527284	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4594518	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4813541	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4813542	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4815337	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4815339	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4815340	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4815341	0.82[ASN][1000 genomes]
rs4815351	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4815355	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4815357	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56312312	0.82[ASN][1000 genomes]
rs6050177	0.82[ASN][1000 genomes]
rs6050179	0.82[ASN][1000 genomes]
rs6050181	0.82[ASN][1000 genomes]
rs6050201	0.82[ASN][1000 genomes]
rs6083684	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083685	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083686	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083688	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083692	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6083699	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083709	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6106975	0.82[ASN][1000 genomes]
rs6106984	0.82[ASN][1000 genomes]
rs6114980	0.82[ASN][1000 genomes]
rs6114981	0.82[ASN][1000 genomes]
rs6114984	0.82[ASN][1000 genomes]
rs6114988	0.82[ASN][1000 genomes]
rs6132773	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132774	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132783	0.86[ASN][1000 genomes]
rs6132785	0.81[AFR][1000 genomes]
rs6138406	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138417	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138423	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138425	0.83[EUR][1000 genomes]
rs6138426	0.83[EUR][1000 genomes]
rs6138427	0.82[EUR][1000 genomes]
rs6138431	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6138435	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138437	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138453	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138458	0.82[ASN][1000 genomes]
rs6138460	0.86[ASN][1000 genomes]
rs6138461	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6138463	0.91[ASN][1000 genomes]
rs7268095	0.82[ASN][1000 genomes]
rs7269416	0.82[ASN][1000 genomes]
rs735886	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8183891	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs926661	0.82[ASN][1000 genomes]
rs926662	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[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

No data

Chromatin state (count:94 , 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	chr20:24975200-24981400	Enhancers	Fetal Intestine Large	intestine
11	chr20:24975800-24983200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:24975800-24986400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr20:24976000-24983200	Weak transcription	Primary B cells from cord blood	blood
14	chr20:24976000-24983200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr20:24976000-24983200	Weak transcription	Fetal Lung	lung
16	chr20:24976000-24983400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr20:24976000-24985000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr20:24976000-24985000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr20:24976000-24985800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr20:24976000-24985800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr20:24976000-24986000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr20:24976000-24986000	Weak transcription	Colonic Mucosa	Colon
23	chr20:24976000-24986400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr20:24976000-24986400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr20:24976000-24987600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr20:24976000-24988000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr20:24976000-24999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr20:24976200-24983200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr20:24976200-24985800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr20:24976200-24985800	Weak transcription	Adipose Nuclei	Adipose
31	chr20:24976200-24985800	Weak transcription	Lung	lung
32	chr20:24976200-24986200	Weak transcription	Dnd41	blood
33	chr20:24976600-24981600	Enhancers	Fetal Intestine Small	intestine
34	chr20:24976800-24983200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr20:24976800-24983200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr20:24976800-24986000	Weak transcription	Brain Germinal Matrix	brain
37	chr20:24977000-24983400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:24977000-24983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr20:24977000-24986600	Weak transcription	Fetal Thymus	thymus
40	chr20:24977200-24983200	Weak transcription	Fetal Stomach	stomach
41	chr20:24978400-24981600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr20:24978400-24981800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr20:24978600-24981600	Enhancers	Fetal Heart	heart
44	chr20:24978600-24981800	Enhancers	Right Ventricle	heart
45	chr20:24978800-24981800	Enhancers	Placenta	Placenta
46	chr20:24978800-24981800	Enhancers	Left Ventricle	heart
47	chr20:24979000-24981600	Enhancers	Brain Hippocampus Middle	brain
48	chr20:24979000-24981800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr20:24979000-24981800	Enhancers	Pancreas	Pancrea
50	chr20:24979000-24987400	Weak transcription	Small Intestine	intestine

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