Variant report

Variant	rs290436
Chromosome Location	chr20:52679492-52679493
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:43)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:43 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52573818..52574952-chr20:52679002..52679930,5	MCF-7	breast:
2	chr20:52212827..52216446-chr20:52677595..52681391,3	MCF-7	breast:
3	chr20:52676834..52679503-chr20:53266669..53268779,2	MCF-7	breast:
4	chr20:52604122..52604816-chr20:52679203..52679933,2	MCF-7	breast:
5	chr20:52365178..52367429-chr20:52678316..52680758,2	MCF-7	breast:
6	chr20:52678920..52679915-chr3:63978931..63979877,3	MCF-7	breast:
7	chr17:56707565..56710367-chr20:52679434..52682124,8	MCF-7	breast:
8	chr20:52531928..52532988-chr20:52679010..52679629,4	MCF-7	breast:
9	chr20:52239693..52240526-chr20:52678812..52679495,2	MCF-7	breast:
10	chr20:52659902..52660887-chr20:52678920..52680381,7	MCF-7	breast:
11	chr20:52679016..52679935-chr20:52814343..52815229,5	MCF-7	breast:
12	chr20:45986431..45988883-chr20:52677453..52680110,2	MCF-7	breast:
13	chr20:46415650..46418405-chr20:52679117..52680920,2	MCF-7	breast:
14	chr20:52679000..52679535-chr20:52692581..52693450,3	MCF-7	breast:
15	chr20:52195174..52196195-chr20:52679020..52679926,4	MCF-7	breast:
16	chr20:52677507..52680494-chr3:64381929..64383896,2	MCF-7	breast:
17	chr20:52573995..52574515-chr20:52679072..52679932,2	MCF-7	breast:
18	chr20:41005640..41008273-chr20:52676406..52679770,3	MCF-7	breast:
19	chr20:52679335..52679944-chr20:52712951..52713861,3	MCF-7	breast:
20	chr20:52674058..52677861-chr20:52678021..52680977,4	K562	blood:
21	chr20:52679438..52680357-chr20:53433878..53434462,2	MCF-7	breast:
22	chr20:52678948..52679961-chr20:53262987..53263883,4	MCF-7	breast:
23	chr20:49404461..49405308-chr20:52679057..52679572,2	MCF-7	breast:
24	chr20:52195073..52195979-chr20:52678957..52680236,7	MCF-7	breast:
25	chr20:52555638..52557146-chr20:52679031..52680345,11	MCF-7	breast:
26	chr17:56736755..56739038-chr20:52679388..52681171,2	MCF-7	breast:
27	chr20:52669724..52670230-chr20:52678961..52679874,2	MCF-7	breast:
28	chr20:52679456..52680456-chr20:52701555..52702068,2	MCF-7	breast:
29	chr20:52678982..52679558-chr20:52709556..52710359,2	MCF-7	breast:
30	chr20:52679231..52682277-chr20:52687139..52688972,3	K562	blood:
31	chr20:52678237..52680834-chr20:52687085..52688960,2	K562	blood:
32	chr20:52678959..52679775-chr20:52815946..52816831,2	MCF-7	breast:
33	chr20:52679369..52679891-chr20:52814598..52815315,2	MCF-7	breast:
34	chr20:52679054..52679922-chr20:52815868..52816606,3	MCF-7	breast:
35	chr20:52679100..52679888-chr20:52713261..52713868,2	MCF-7	breast:
36	chr20:52556238..52557068-chr20:52678971..52679960,5	MCF-7	breast:
37	chr20:46750253..46752428-chr20:52678041..52680092,2	MCF-7	breast:
38	chr20:52559378..52561018-chr20:52678965..52680200,31	MCF-7	breast:
39	chr20:52190970..52191876-chr20:52678761..52679613,2	MCF-7	breast:
40	chr20:52556569..52566193-chr20:52677353..52682397,12	MCF-7	breast:
41	chr20:52559216..52560998-chr20:52678738..52679912,14	MCF-7	breast:
42	chr20:52561105..52561751-chr20:52678984..52679783,3	MCF-7	breast:
43	chr20:52678972..52680191-chr20:55818951..55820251,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266826	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000236352	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs103926	0.85[ASN][1000 genomes]
rs290391	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs290392	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs290393	0.90[CHB][hapmap]
rs290430	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290431	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290432	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290441	0.83[ASN][1000 genomes]
rs290444	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs290445	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs290446	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs290448	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs290449	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs458674	1.00[ASN][1000 genomes]
rs459113	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs460317	1.00[ASN][1000 genomes]
rs460470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs462174	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs463420	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs463722	0.94[ASN][1000 genomes]
rs467267	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs467321	1.00[ASN][1000 genomes]
rs756021	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	esv2756743	chr20:52679137-52685208	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2758801	chr20:52679137-52685208	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs290436	NEUROD4	trans	parietal	SCAN
rs290436	BCAS1	Cis_1M	lymphoblastoid	RTeQTL
rs290436	BCAS1	cis	multi-tissue	Pritchard
rs290436	BCAS1	cis	Lymphoblastoid	GTEx
rs290436	BCAS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:52669400-52681800	Weak transcription	Gastric	stomach
3	chr20:52674400-52681200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52674400-52682000	Weak transcription	Colonic Mucosa	Colon
5	chr20:52675000-52683000	Weak transcription	HepG2	liver
6	chr20:52675600-52679600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr20:52675800-52679600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr20:52677200-52680000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr20:52677400-52680200	Enhancers	Stomach Mucosa	stomach
10	chr20:52677600-52679800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:52677600-52679800	Enhancers	HSMMtube	muscle
12	chr20:52677600-52679800	Enhancers	NHDF-Ad	bronchial
13	chr20:52677800-52679800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr20:52677800-52679800	Enhancers	Brain Cingulate Gyrus	brain
15	chr20:52677800-52679800	Enhancers	Brain Substantia Nigra	brain
16	chr20:52677800-52680000	Enhancers	Adipose Nuclei	Adipose
17	chr20:52678000-52679800	Enhancers	Fetal Heart	heart
18	chr20:52678200-52680200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:52678200-52683800	Weak transcription	HMEC	breast
20	chr20:52678200-52684400	Weak transcription	Fetal Stomach	stomach
21	chr20:52678400-52683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:52678800-52680000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr20:52679000-52679800	Enhancers	Brain Angular Gyrus	brain
24	chr20:52679000-52679800	Enhancers	Brain Hippocampus Middle	brain
25	chr20:52679000-52679800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr20:52679000-52680000	Enhancers	A549	lung
27	chr20:52679200-52679600	Enhancers	Brain Anterior Caudate	brain
28	chr20:52679200-52679800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr20:52679200-52679800	Enhancers	K562	blood
30	chr20:52679200-52680200	Enhancers	GM12878-XiMat	blood
31	chr20:52679200-52680800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr20:52679200-52681600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr20:52679400-52683000	Weak transcription	HSMM	muscle
34	chr20:52679400-52683000	Weak transcription	NH-A	brain

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