Variant report

Variant	rs6078509
Chromosome Location	chr20:1282285-1282286
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1279418..1283217-chr20:1283449..1287758,5	K562	blood:
2	chr20:1282248..1284954-chr20:1288783..1291101,2	MCF-7	breast:
3	chr20:1280644..1283563-chr20:1283914..1285559,2	MCF-7	breast:
4	chr20:1281423..1283535-chr20:1306063..1308157,2	K562	blood:

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction
ENSG00000234684	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12624336	0.87[ASN][1000 genomes]
rs3764715	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3795140	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3795141	0.92[ASN][1000 genomes]
rs3795142	0.92[ASN][1000 genomes]
rs3818331	0.92[ASN][1000 genomes]
rs6109320	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134520	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs912104	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs912108	0.92[EUR][1000 genomes]
rs966846	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1067360	chr20:1245753-1283508	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1067393	chr20:1254805-1302796	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv912588	chr20:1269588-1300456	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv912589	chr20:1272686-1298397	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv912590	chr20:1278770-1298397	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3437211	chr20:1280452-1285150	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
9	esv3441111	chr20:1281052-1284350	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
10	esv3415895	chr20:1281152-1284350	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
11	esv3361547	chr20:1281252-1284350	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
12	esv3378514	chr20:1281252-1284350	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1253800-1285400	Weak transcription	Aorta	Aorta
2	chr20:1266400-1284800	Weak transcription	Brain Germinal Matrix	brain
3	chr20:1269200-1283600	Weak transcription	Right Ventricle	heart
4	chr20:1269400-1283200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:1272200-1285400	Weak transcription	Adipose Nuclei	Adipose
6	chr20:1272200-1285400	Weak transcription	Left Ventricle	heart
7	chr20:1272200-1286000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:1272400-1285800	Weak transcription	Fetal Muscle Leg	muscle
9	chr20:1272600-1294000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr20:1272800-1283400	Weak transcription	HSMMtube	muscle
11	chr20:1273000-1294000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr20:1274800-1288200	Weak transcription	Fetal Intestine Small	intestine
13	chr20:1275000-1289400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr20:1275400-1284000	Weak transcription	Pancreas	Pancrea
15	chr20:1275800-1285400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr20:1275800-1293800	Weak transcription	Brain Substantia Nigra	brain
17	chr20:1276600-1289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr20:1278200-1294000	Weak transcription	Colon Smooth Muscle	Colon
19	chr20:1278800-1283600	Weak transcription	Fetal Brain Female	brain
20	chr20:1280400-1282400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr20:1280600-1294000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr20:1281400-1289800	Weak transcription	Colonic Mucosa	Colon
23	chr20:1281600-1283400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr20:1281600-1283400	Weak transcription	Brain Angular Gyrus	brain
25	chr20:1281600-1285600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr20:1281600-1285600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr20:1281600-1285800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr20:1281600-1290000	Weak transcription	Brain Hippocampus Middle	brain
29	chr20:1281800-1283600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr20:1281800-1283600	Weak transcription	Gastric	stomach
31	chr20:1281800-1285200	Weak transcription	Lung	lung
32	chr20:1281800-1294000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr20:1282000-1282400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr20:1282000-1283200	Weak transcription	Primary T cells from cord blood	blood
35	chr20:1282000-1283200	Weak transcription	Osteobl	bone
36	chr20:1282000-1283400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr20:1282000-1283400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:1282000-1283600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr20:1282000-1283600	Weak transcription	HSMM	muscle
40	chr20:1282000-1283800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr20:1282000-1284000	Weak transcription	Brain Anterior Caudate	brain
42	chr20:1282000-1284600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:1282000-1284600	Weak transcription	Fetal Stomach	stomach
44	chr20:1282000-1285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr20:1282000-1285800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr20:1282000-1289000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:1282000-1293800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr20:1282000-1293800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr20:1282000-1294000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr20:1282000-1294400	Weak transcription	Stomach Mucosa	stomach

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