Variant report

Variant	rs2762920
Chromosome Location	chr20:52749823-52749824
allele	A/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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:57922783..57925093-chr20:52747616..52750440,2	MCF-7	breast:
2	chr17:57913131..57926939-chr20:52735776..52751538,42	MCF-7	breast:
3	chr20:52732059..52732575-chr20:52749314..52750086,2	MCF-7	breast:
4	chr20:46640095..46644047-chr20:52746837..52750756,3	MCF-7	breast:
5	chr20:46413224..46418685-chr20:52746491..52752686,10	MCF-7	breast:
6	chr12:52636521..52638723-chr20:52748359..52750383,2	MCF-7	breast:
7	chr12:53344317..53347285-chr20:52748753..52751041,2	MCF-7	breast:
8	chr17:57927648..57930495-chr20:52747447..52749860,2	MCF-7	breast:
9	chr20:52748698..52751291-chr5:43063719..43066495,2	MCF-7	breast:
10	chr17:56735202..56737939-chr20:52748696..52751920,4	MCF-7	breast:
11	chr20:52720110..52720627-chr20:52749159..52749899,2	MCF-7	breast:
12	chr17:56736366..56738088-chr20:52748194..52751006,3	MCF-7	breast:
13	chr20:46417525..46420204-chr20:52747771..52750602,2	MCF-7	breast:
14	chr20:52720225..52723216-chr20:52749431..52752183,2	K562	blood:
15	chr20:46616780..46618691-chr20:52748141..52750829,2	MCF-7	breast:
16	chr17:56707619..56710651-chr20:52747363..52752620,6	MCF-7	breast:
17	chr20:52740077..52741098-chr20:52749020..52749938,3	MCF-7	breast:
18	chr17:56704127..56711907-chr20:52729106..52752952,70	MCF-7	breast:
19	chr20:52747148..52749996-chr4:40425542..40427397,2	MCF-7	breast:
20	chr20:52747406..52750042-chr20:52765504..52767989,2	K562	blood:
21	chr20:52749818..52752750-chr5:43554749..43557451,2	MCF-7	breast:
22	chr15:63794674..63797406-chr20:52748938..52750854,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000237423	Chromatin interaction
ENSG00000135480	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000111057	Chromatin interaction
ENSG00000265039	Chromatin interaction
ENSG00000140455	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000225410	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000199004	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2585412	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2585447	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2585448	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2585449	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2585451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616277	0.82[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616278	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616279	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2762918	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2762919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2762921	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2762932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2762933	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2762934	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2762935	0.91[ASN][1000 genomes]
rs6022987	0.91[ASN][1000 genomes]
rs751088	0.93[ASN][1000 genomes]

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	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
2	nsv586280	chr20:52718555-52758416	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	84 gene(s)	inside rSNPs	diseases
3	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2762920	LOC284751	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52748000-52750400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:52748200-52750000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr20:52748200-52750200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:52748200-52750200	Enhancers	Placenta	Placenta
5	chr20:52748200-52750400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:52748200-52751800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:52748200-52751800	Enhancers	HMEC	breast
8	chr20:52748400-52750600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr20:52748400-52750600	Flanking Active TSS	HepG2	liver
10	chr20:52748400-52750800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr20:52748400-52751400	Enhancers	NHLF	lung
12	chr20:52748600-52750000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr20:52748800-52750400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr20:52748800-52751000	Flanking Active TSS	A549	lung
15	chr20:52748800-52751600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:52749000-52750000	Enhancers	Duodenum Mucosa	Duodenum
17	chr20:52749000-52750200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr20:52749200-52750000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr20:52749200-52750000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:52749200-52750000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr20:52749200-52750000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr20:52749200-52750000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr20:52749200-52750000	Enhancers	Fetal Kidney	kidney
24	chr20:52749200-52750200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr20:52749200-52750200	Enhancers	Fetal Muscle Leg	muscle
26	chr20:52749400-52750000	Enhancers	Adipose Nuclei	Adipose
27	chr20:52749400-52750000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr20:52749400-52750200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr20:52749400-52750200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr20:52749400-52750400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:52749400-52751400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr20:52749400-52751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:52749400-52751800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr20:52749600-52750000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr20:52749600-52750000	Flanking Active TSS	HSMMtube	muscle
36	chr20:52749600-52750200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:52749600-52750200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:52749600-52750200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr20:52749600-52750200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr20:52749600-52750200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr20:52749600-52750200	Flanking Active TSS	Hela-S3	cervix
42	chr20:52749600-52750400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr20:52749600-52750400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr20:52749600-52750400	Flanking Active TSS	NHDF-Ad	bronchial
45	chr20:52749600-52750400	Flanking Active TSS	Osteobl	bone
46	chr20:52749600-52750600	Enhancers	Brain Hippocampus Middle	brain
47	chr20:52749800-52750000	Enhancers	Brain Anterior Caudate	brain
48	chr20:52749800-52750000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr20:52749800-52750000	Enhancers	Small Intestine	intestine
50	chr20:52749800-52750000	Enhancers	NH-A	brain

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