Variant report

Variant	rs6063975
Chromosome Location	chr20:52278275-52278276
allele	C/G
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:48)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:48 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52278273..52278907-chr20:52295890..52296446,2	MCF-7	breast:
2	chr20:52278052..52278913-chr20:52295859..52296841,4	MCF-7	breast:
3	chr20:52278028..52278967-chr20:52402219..52403203,5	MCF-7	breast:
4	chr17:59800235..59800998-chr20:52278053..52278971,3	MCF-7	breast:
5	chr20:52278028..52279035-chr20:52327271..52328369,11	MCF-7	breast:
6	chr20:52278028..52278937-chr20:52811392..52812502,5	MCF-7	breast:
7	chr20:52277725..52279357-chr7:72970513..72973194,2	MCF-7	breast:
8	chr17:59475937..59477859-chr20:52276880..52278926,2	MCF-7	breast:
9	chr20:52278066..52278981-chr20:52357949..52358822,3	MCF-7	breast:
10	chr20:52278275..52278962-chr20:52390065..52390855,2	MCF-7	breast:
11	chr20:52278044..52278974-chr7:101647121..101648013,2	MCF-7	breast:
12	chr20:49343995..49344510-chr20:52278099..52278858,2	MCF-7	breast:
13	chr20:52238044..52238679-chr20:52278083..52278868,2	MCF-7	breast:
14	chr20:45985766..45988704-chr20:52276901..52279846,3	MCF-7	breast:
15	chr20:52277928..52278961-chr3:32489011..32489511,3	MCF-7	breast:
16	chr20:52278068..52279052-chr20:55837939..55839139,4	MCF-7	breast:
17	chr20:52276634..52278992-chr20:52292801..52294676,2	K562	blood:
18	chr20:52277654..52278913-chr20:52296328..52297068,3	MCF-7	breast:
19	chr20:52224435..52225427-chr20:52278008..52279011,24	MCF-7	breast:
20	chr20:52278050..52278914-chr20:52739934..52740849,4	MCF-7	breast:
21	chr20:46619897..46622713-chr20:52276800..52278614,2	MCF-7	breast:
22	chr20:52277347..52278945-chr20:52765329..52766278,10	MCF-7	breast:
23	chr20:52277294..52279004-chr20:52341320..52342426,29	MCF-7	breast:
24	chr20:52278094..52278874-chr20:52765343..52766265,2	MCF-7	breast:
25	chr15:64237957..64238498-chr20:52278114..52278867,2	MCF-7	breast:
26	chr20:52195567..52196120-chr20:52278101..52278912,2	MCF-7	breast:
27	chr17:56716876..56717591-chr20:52278075..52278814,2	MCF-7	breast:
28	chr20:52278028..52278954-chr20:52811294..52812502,10	MCF-7	breast:
29	chr20:52238544..52239393-chr20:52278148..52278651,2	MCF-7	breast:
30	chr20:52278061..52278601-chr20:52599248..52600106,2	MCF-7	breast:
31	chr20:52224515..52225427-chr20:52278079..52279008,9	MCF-7	breast:
32	chr17:59800235..59800999-chr20:52278081..52278971,3	MCF-7	breast:
33	chr20:52209870..52210455-chr20:52277768..52278453,2	MCF-7	breast:
34	chr1:182353766..182355662-chr20:52277139..52279207,2	MCF-7	breast:
35	chr20:45949990..45952457-chr20:52276718..52278460,2	MCF-7	breast:
36	chr20:52278055..52279007-chr20:52402723..52403658,3	MCF-7	breast:
37	chr20:52278001..52278960-chr20:52341336..52342351,16	MCF-7	breast:
38	chr20:52275241..52279422-chr20:55839192..55841945,5	MCF-7	breast:
39	chr20:52277378..52279205-chr20:55847044..55849941,2	MCF-7	breast:
40	chr17:77793092..77795595-chr20:52275872..52278371,2	MCF-7	breast:
41	chr20:52239835..52240474-chr20:52277583..52278444,2	MCF-7	breast:
42	chr20:52278107..52278961-chr4:135702927..135703705,2	MCF-7	breast:
43	chr20:52278188..52278952-chr20:52402415..52403122,5	MCF-7	breast:
44	chr20:52238681..52239274-chr20:52278222..52278871,2	MCF-7	breast:
45	chr20:52278079..52279035-chr20:52327271..52328369,9	MCF-7	breast:
46	chr20:52278080..52279014-chr20:52532287..52532875,2	MCF-7	breast:
47	chr20:52277828..52280827-chr7:7693453..7695076,2	MCF-7	breast:
48	chr20:52278103..52278773-chr20:52444653..52445447,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000121068	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000135821	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000106635	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12481286	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12624860	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12625046	0.85[ASN][1000 genomes]
rs13039563	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4586691	0.84[ASN][1000 genomes]
rs6013752	0.90[ASN][1000 genomes]
rs6022654	0.91[ASN][1000 genomes]
rs6022656	0.91[ASN][1000 genomes]
rs6068620	0.81[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	nsv1055342	chr20:52126973-52352323	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	214 gene(s)	inside rSNPs	diseases
2	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
3	nsv834006	chr20:52182498-52309366	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	193 gene(s)	inside rSNPs	diseases
4	nsv586209	chr20:52204062-52289243	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	160 gene(s)	inside rSNPs	diseases
5	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
6	nsv912935	chr20:52221906-52337118	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	101 gene(s)	inside rSNPs	diseases
7	nsv912936	chr20:52250876-52344962	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
8	nsv912937	chr20:52251863-52344962	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
10	nsv517172	chr20:52276452-52289243	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
11	nsv518277	chr20:52276452-52315311	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
12	nsv912938	chr20:52276452-52328338	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52276600-52278400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr20:52276800-52278600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:52276800-52278600	Enhancers	Dnd41	blood
4	chr20:52276800-52278600	Flanking Active TSS	GM12878-XiMat	blood
5	chr20:52277000-52278400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr20:52277000-52278400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:52277000-52278400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr20:52277000-52278600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr20:52277000-52279600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr20:52277000-52290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr20:52277200-52278400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr20:52277200-52278400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:52277200-52278400	Enhancers	Duodenum Mucosa	Duodenum
14	chr20:52277200-52278400	Enhancers	Placenta	Placenta
15	chr20:52277200-52278400	Enhancers	Left Ventricle	heart
16	chr20:52277200-52278400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr20:52277200-52278400	Enhancers	NHLF	lung
18	chr20:52277200-52278600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr20:52277200-52278600	Enhancers	Liver	Liver
20	chr20:52277400-52278400	Enhancers	Primary B cells from peripheral blood	blood
21	chr20:52277400-52278400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr20:52277400-52278400	Enhancers	Brain Angular Gyrus	brain
23	chr20:52277400-52278400	Enhancers	Brain Cingulate Gyrus	brain
24	chr20:52277400-52278400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr20:52277400-52278400	Enhancers	Brain Substantia Nigra	brain
26	chr20:52277400-52278400	Enhancers	Fetal Intestine Large	intestine
27	chr20:52277400-52278400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr20:52277400-52278400	Enhancers	Right Atrium	heart
29	chr20:52277400-52278400	Enhancers	NHEK	skin
30	chr20:52277400-52278400	Enhancers	Osteobl	bone
31	chr20:52277400-52278600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:52277400-52278600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr20:52277400-52278600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr20:52277400-52278600	Enhancers	Brain Hippocampus Middle	brain
35	chr20:52277400-52278600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr20:52277400-52278600	Enhancers	Fetal Intestine Small	intestine
37	chr20:52277400-52278600	Enhancers	Fetal Stomach	stomach
38	chr20:52277400-52278600	Flanking Active TSS	HepG2	liver
39	chr20:52277400-52278800	Enhancers	Fetal Muscle Leg	muscle
40	chr20:52277400-52279400	Enhancers	Primary B cells from cord blood	blood
41	chr20:52277400-52279400	Enhancers	Primary hematopoietic stem cells	blood
42	chr20:52277400-52279400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr20:52277400-52280000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr20:52277600-52278400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr20:52277600-52278400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr20:52277600-52278400	Weak transcription	Colonic Mucosa	Colon
47	chr20:52277600-52278400	Enhancers	Thymus	Thymus
48	chr20:52277600-52278600	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr20:52277600-52278600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr20:52277600-52278600	Enhancers	Stomach Smooth Muscle	stomach

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