Variant report

Variant	rs6138533
Chromosome Location	chr20:25174130-25174131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25174010..25179528-chr20:25225802..25231331,13	MCF-7	breast:
2	chr20:25173813..25179807-chr20:25203379..25207002,9	MCF-7	breast:
3	chr20:25166380..25169258-chr20:25173266..25174773,2	K562	blood:

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1108811	0.93[EUR][1000 genomes]
rs11698226	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11699149	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11699219	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11699614	0.95[EUR][1000 genomes]
rs13036626	0.85[ASN][1000 genomes]
rs13037201	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13037374	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13039237	0.90[EUR][1000 genomes]
rs13041051	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13043906	0.93[EUR][1000 genomes]
rs13045481	0.82[EUR][1000 genomes]
rs2038182	0.84[ASN][1000 genomes]
rs2103715	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2235770	0.96[EUR][1000 genomes]
rs2892314	0.93[EUR][1000 genomes]
rs34242837	0.82[EUR][1000 genomes]
rs35047430	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35231728	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36115891	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815388	0.84[ASN][1000 genomes]
rs4815389	0.84[ASN][1000 genomes]
rs4815392	0.88[ASN][1000 genomes]
rs6037038	0.93[EUR][1000 genomes]
rs6037049	0.84[ASN][1000 genomes]
rs6037052	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050390	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050397	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6050399	0.84[ASN][1000 genomes]
rs6050400	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050403	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050404	0.85[ASN][1000 genomes]
rs6050406	0.83[ASN][1000 genomes]
rs6050408	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6050409	0.83[ASN][1000 genomes]
rs6050410	0.92[ASN][1000 genomes]
rs6050411	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050412	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050413	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6050415	0.91[ASN][1000 genomes]
rs6050418	0.91[ASN][1000 genomes]
rs6050419	0.91[ASN][1000 genomes]
rs6050421	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6107013	0.94[ASN][1000 genomes]
rs6115069	0.84[ASN][1000 genomes]
rs6132804	0.95[EUR][1000 genomes]
rs6132810	0.96[EUR][1000 genomes]
rs6132812	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132816	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6138492	0.90[EUR][1000 genomes]
rs6138493	0.93[EUR][1000 genomes]
rs6138496	0.93[EUR][1000 genomes]
rs6138510	0.97[EUR][1000 genomes]
rs6138511	0.90[EUR][1000 genomes]
rs6138519	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138520	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138521	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138528	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138530	0.85[ASN][1000 genomes]
rs6138531	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6138532	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6515614	0.91[ASN][1000 genomes]
rs8119777	0.94[EUR][1000 genomes]
rs910101	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv3340	chr20:25160137-25190540	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	esv1002059	chr20:25164737-25175153	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25168200-25175800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:25168800-25175200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:25169200-25175600	Weak transcription	Fetal Lung	lung
4	chr20:25169400-25175200	Weak transcription	Lung	lung
5	chr20:25169400-25175600	Weak transcription	Gastric	stomach
6	chr20:25171400-25175600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr20:25171600-25175200	Weak transcription	Right Ventricle	heart
8	chr20:25171800-25175600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:25172000-25175200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr20:25172200-25175800	Weak transcription	Psoas Muscle	Psoas
11	chr20:25172600-25175600	Weak transcription	HMEC	breast
12	chr20:25172800-25175600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:25173000-25175200	Weak transcription	Left Ventricle	heart
14	chr20:25173000-25175400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr20:25173000-25175400	Weak transcription	Pancreas	Pancrea
16	chr20:25173000-25175600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr20:25173000-25175600	Weak transcription	Placenta	Placenta
18	chr20:25173000-25175800	Weak transcription	Right Atrium	heart
19	chr20:25173200-25175800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:25173200-25176000	Weak transcription	Ovary	ovary
21	chr20:25173400-25175000	Weak transcription	Fetal Heart	heart
22	chr20:25173400-25175400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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