Variant report

Variant	rs158546
Chromosome Location	chr20:52641434-52641435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52638922..52641694-chr20:52671102..52673075,2	MCF-7	breast:
2	chr20:52640367..52641889-chr20:52645625..52647973,2	K562	blood:
3	chr20:52637571..52639350-chr20:52639396..52641959,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11699406	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs158539	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158550	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs208642	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs208644	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2299720	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs290384	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290386	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290388	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290417	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290456	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290457	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290458	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290459	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290462	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290466	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290471	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71623	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	esv2763673	chr20:52637074-52668126	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv3419	chr20:52637581-52672115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52634800-52645400	Weak transcription	Fetal Lung	lung
4	chr20:52635800-52641800	Enhancers	Brain Substantia Nigra	brain
5	chr20:52640400-52642200	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr20:52640600-52641600	Strong transcription	Stomach Mucosa	stomach
7	chr20:52640800-52642000	Enhancers	Brain Cingulate Gyrus	brain
8	chr20:52640800-52643800	Enhancers	Fetal Brain Male	brain
9	chr20:52641000-52642000	Enhancers	NHDF-Ad	bronchial
10	chr20:52641000-52643200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:52641000-52643400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr20:52641200-52641600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:52641200-52641600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr20:52641200-52642000	Enhancers	HSMMtube	muscle
15	chr20:52641200-52642400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr20:52641200-52642400	Enhancers	Osteobl	bone
17	chr20:52641200-52644400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr20:52641400-52641600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr20:52641400-52641800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:52641400-52641800	Weak transcription	Brain Angular Gyrus	brain
21	chr20:52641400-52641800	Enhancers	Fetal Kidney	kidney
22	chr20:52641400-52642000	Enhancers	Colon Smooth Muscle	Colon
23	chr20:52641400-52642400	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr20:52641400-52642600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr20:52641400-52642600	Enhancers	NH-A	brain
26	chr20:52641400-52646000	Active TSS	Brain Anterior Caudate	brain

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