Variant report

Variant	rs4811485
Chromosome Location	chr20:52552780-52552781
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52367670..52370398-chr20:52548161..52552939,6	K562	blood:
2	chr17:57109264..57111051-chr20:52551167..52554043,2	MCF-7	breast:
3	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
4	chr20:52469682..52472418-chr20:52551027..52553100,2	K562	blood:
5	chr20:52195254..52195975-chr20:52552317..52553030,2	MCF-7	breast:
6	chr20:52551078..52553567-chr20:55847607..55851332,6	MCF-7	breast:
7	chr17:59711920..59714434-chr20:52552596..52554314,2	MCF-7	breast:
8	chr17:57921749..57924885-chr20:52550467..52553589,3	MCF-7	breast:
9	chr20:52552477..52556062-chr3:64098052..64101134,3	MCF-7	breast:
10	chr20:45985786..45987562-chr20:52552557..52555043,2	MCF-7	breast:
11	chr20:52550372..52553297-chr20:52685903..52688143,2	MCF-7	breast:
12	chr17:59472113..59474358-chr20:52552537..52554106,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000064787	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16998572	0.89[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs16998584	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299733	1.00[ASW][hapmap]
rs4809945	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6013838	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127029	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4811485	NCRNA00200	trans	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52538400-52553400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:52543600-52556000	Weak transcription	Aorta	Aorta
3	chr20:52543800-52555000	Weak transcription	Stomach Mucosa	stomach
4	chr20:52549000-52558800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr20:52549400-52553800	Enhancers	Primary hematopoietic stem cells	blood
6	chr20:52550000-52552800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr20:52550000-52552800	Enhancers	Primary T cells from cord blood	blood
8	chr20:52550000-52556800	Enhancers	Primary B cells from peripheral blood	blood
9	chr20:52550200-52553000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr20:52550200-52555000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:52550400-52557400	Enhancers	Placenta	Placenta
12	chr20:52550800-52555400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr20:52551000-52552800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr20:52551000-52552800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr20:52551200-52553000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr20:52551200-52553600	Weak transcription	Ovary	ovary
17	chr20:52551200-52556200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr20:52551200-52556400	Weak transcription	Psoas Muscle	Psoas
19	chr20:52551400-52553000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr20:52551600-52553000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr20:52551600-52553000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr20:52551600-52553600	Weak transcription	Fetal Intestine Large	intestine
23	chr20:52551600-52555800	Weak transcription	Colon Smooth Muscle	Colon
24	chr20:52551800-52552800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr20:52551800-52555400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:52551800-52555400	Weak transcription	NHEK	skin
27	chr20:52551800-52556200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:52551800-52557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr20:52552000-52552800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr20:52552000-52553000	Enhancers	Primary B cells from cord blood	blood
31	chr20:52552000-52553600	Enhancers	K562	blood
32	chr20:52552000-52555000	Weak transcription	A549	lung
33	chr20:52552000-52555200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr20:52552000-52555400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:52552000-52555400	Weak transcription	HMEC	breast
36	chr20:52552000-52555600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr20:52552000-52555600	Weak transcription	Brain Angular Gyrus	brain
38	chr20:52552000-52556000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr20:52552000-52556000	Weak transcription	NH-A	brain
40	chr20:52552000-52556800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr20:52552200-52553400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr20:52552200-52553400	Weak transcription	NHDF-Ad	bronchial
44	chr20:52552200-52553600	Weak transcription	Fetal Stomach	stomach
45	chr20:52552200-52555400	Weak transcription	Brain Hippocampus Middle	brain
46	chr20:52552200-52555400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr20:52552200-52555400	Weak transcription	NHLF	lung
48	chr20:52552200-52555600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr20:52552200-52555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr20:52552200-52555600	Weak transcription	Rectal Mucosa Donor 31	rectum

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