Variant report

Variant	rs6123304
Chromosome Location	chr20:52279092-52279093
allele	A/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	chr20:52277725..52279357-chr7:72970513..72973194,2	MCF-7	breast:
2	chr20:45985766..45988704-chr20:52276901..52279846,3	MCF-7	breast:
3	chr20:52195959..52198934-chr20:52278537..52280867,2	K562	blood:
4	chr20:52278291..52280795-chr3:49064325..49066546,2	MCF-7	breast:
5	chr15:51177817..51178676-chr20:52278485..52279434,2	MCF-7	breast:
6	chr1:182353766..182355662-chr20:52277139..52279207,2	MCF-7	breast:
7	chr20:52275241..52279422-chr20:55839192..55841945,5	MCF-7	breast:
8	chr20:52277378..52279205-chr20:55847044..55849941,2	MCF-7	breast:
9	chr20:52277828..52280827-chr7:7693453..7695076,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000135821	Chromatin interaction
ENSG00000106635	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs34537877	0.81[ASN][1000 genomes]
rs35241466	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56269299	0.84[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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52277000-52279600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr20:52277000-52290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:52277400-52279400	Enhancers	Primary B cells from cord blood	blood
4	chr20:52277400-52279400	Enhancers	Primary hematopoietic stem cells	blood
5	chr20:52277400-52279400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr20:52277400-52280000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr20:52277600-52279200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr20:52277600-52279400	Enhancers	Fetal Thymus	thymus
9	chr20:52277600-52279600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr20:52277800-52279200	Weak transcription	HUVEC	blood vessel
11	chr20:52277800-52279400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr20:52277800-52279400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr20:52277800-52279600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr20:52277800-52279800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr20:52277800-52280200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr20:52277800-52283200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr20:52278000-52279400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr20:52278000-52279800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr20:52278200-52279600	Enhancers	Primary T cells from cord blood	blood
20	chr20:52278200-52280600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr20:52278400-52279200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr20:52278400-52279800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr20:52278400-52279800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr20:52278400-52280600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr20:52278400-52281000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr20:52278400-52289400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr20:52278600-52279200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr20:52278600-52279800	Enhancers	GM12878-XiMat	blood
29	chr20:52278600-52279800	Enhancers	HepG2	liver
30	chr20:52278600-52280600	Weak transcription	A549	lung
31	chr20:52278600-52280800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:52278600-52280800	Weak transcription	Fetal Lung	lung
33	chr20:52278800-52279400	Weak transcription	Fetal Muscle Leg	muscle
34	chr20:52279000-52279400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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