Variant report

Variant	rs1538445
Chromosome Location	chr20:23184826-23184827
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23183062..23185782-chr20:23330509..23332996,2	MCF-7	breast:
2	chr20:23181724..23187567-chr20:23190860..23194115,6	MCF-7	breast:
3	chr20:23131349..23133053-chr20:23183942..23185506,2	K562	blood:
4	chr20:23131411..23133053-chr20:23183792..23185506,2	K562	blood:
5	chr20:23178876..23181209-chr20:23183336..23185495,2	K562	blood:

Variant related genes	Relation type
ENSG00000234832	Chromatin interaction
ENSG00000132661	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1005856	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1099456	0.87[AMR][1000 genomes]
rs11696272	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11896	0.94[ASN][1000 genomes]
rs1338943	0.90[ASN][1000 genomes]
rs1538446	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1856470	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2024897	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4813483	0.90[ASN][1000 genomes]
rs6036338	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6048590	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6048591	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6048592	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6048595	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6048612	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6048615	0.80[EUR][1000 genomes]
rs6048618	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6048619	0.80[EUR][1000 genomes]
rs6076035	0.95[ASN][1000 genomes]
rs6076038	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6076039	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6076040	0.94[ASN][1000 genomes]
rs6083030	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083031	0.94[ASN][1000 genomes]
rs6083032	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083033	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083036	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083038	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083043	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6083044	0.97[ASN][1000 genomes]
rs6083047	0.96[ASN][1000 genomes]
rs6083050	0.94[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs6106615	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6106616	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6106617	0.91[ASN][1000 genomes]
rs6106619	0.91[ASN][1000 genomes]
rs6113992	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6114001	0.94[ASN][1000 genomes]
rs6114004	0.91[ASN][1000 genomes]
rs6132573	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132576	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132577	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132579	0.81[AMR][1000 genomes]
rs62206882	0.86[AMR][1000 genomes]
rs62206883	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs750652	0.87[AMR][1000 genomes]
rs750653	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8118328	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs844924	0.88[AMR][1000 genomes]
rs844929	0.84[AMR][1000 genomes]
rs844932	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs844934	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs844935	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844936	0.84[AMR][1000 genomes]
rs844937	0.81[CEU][hapmap];0.87[AMR][1000 genomes]
rs844938	0.87[AMR][1000 genomes]
rs844939	0.82[CEU][hapmap];0.87[AMR][1000 genomes]
rs844940	0.87[AMR][1000 genomes]
rs844941	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs844942	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs867909	0.80[EUR][1000 genomes]
rs870225	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912817	chr20:23127661-23240969	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066734	chr20:23170094-23277628	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23181800-23185000	Weak transcription	Esophagus	oesophagus
2	chr20:23182000-23185000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23182000-23186600	Weak transcription	Lung	lung
4	chr20:23182200-23185000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr20:23182200-23185000	Weak transcription	Placenta	Placenta
6	chr20:23182200-23185600	Weak transcription	Stomach Mucosa	stomach
7	chr20:23182600-23185000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:23182600-23185000	Weak transcription	Left Ventricle	heart
9	chr20:23182600-23186200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr20:23182600-23187800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:23182800-23185800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr20:23183000-23186600	Enhancers	Colon Smooth Muscle	Colon
13	chr20:23183400-23186000	Enhancers	Stomach Smooth Muscle	stomach
14	chr20:23183600-23186600	Enhancers	Rectal Smooth Muscle	rectum
15	chr20:23183600-23187000	Enhancers	Brain Substantia Nigra	brain
16	chr20:23183600-23187000	Enhancers	Fetal Heart	heart
17	chr20:23183600-23189000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:23183800-23185000	Weak transcription	Brain Anterior Caudate	brain
19	chr20:23183800-23185200	Weak transcription	Right Ventricle	heart
20	chr20:23183800-23185400	Weak transcription	Brain Angular Gyrus	brain
21	chr20:23183800-23185400	Weak transcription	Fetal Stomach	stomach
22	chr20:23183800-23185800	Weak transcription	Right Atrium	heart
23	chr20:23183800-23186000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr20:23183800-23186600	Weak transcription	Psoas Muscle	Psoas
25	chr20:23184000-23186600	Weak transcription	NHDF-Ad	bronchial
26	chr20:23184200-23185200	Weak transcription	Brain Hippocampus Middle	brain
27	chr20:23184200-23185200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr20:23184200-23185600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr20:23184200-23185800	Weak transcription	HSMMtube	muscle
30	chr20:23184200-23186400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr20:23184200-23186600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr20:23184400-23185400	Weak transcription	Adipose Nuclei	Adipose
33	chr20:23184600-23185600	Enhancers	K562	blood
34	chr20:23184800-23185200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr20:23184800-23185200	Enhancers	Fetal Kidney	kidney
36	chr20:23184800-23185800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr20:23184800-23185800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr20:23184800-23185800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr20:23184800-23186000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr20:23184800-23186800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr20:23184800-23187000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr20:23184800-23187200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
43	chr20:23184800-23187200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr20:23184800-23187400	Enhancers	Fetal Lung	lung
45	chr20:23184800-23187800	Enhancers	Brain Germinal Matrix	brain
46	chr20:23184800-23188400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr20:23184800-23189000	Enhancers	Fetal Muscle Leg	muscle

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