Variant report

Variant	rs2299718
Chromosome Location	chr20:52633683-52633684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:52581180..52583865-chr20:52632082..52634620,2	MCF-7	breast:
2	chr20:52628442..52630921-chr20:52632411..52634269,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11905945	1.00[CEU][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1381983	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1381984	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1557853	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2072128	1.00[CEU][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2107327	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2189502	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2214530	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2238701	0.80[AMR][1000 genomes]
rs2276487	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276488	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276489	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276491	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299698	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2299699	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2299701	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2299702	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2299704	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs2299705	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2299707	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2299711	1.00[CEU][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2299712	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2299715	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2299717	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2870304	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34973146	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35883829	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3819585	0.94[ASN][1000 genomes]
rs6091807	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6091808	0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs6091811	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6091812	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6097749	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6123345	1.00[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127058	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6127060	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127061	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6127062	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6127063	1.00[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127065	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6127066	0.94[EUR][1000 genomes]
rs6127068	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6127072	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6127073	0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67082409	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71323984	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73133436	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs732344	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs765348	0.81[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	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

No data

Chromatin state (count:24 , 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	chr20:52631400-52634400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:52631400-52635800	Weak transcription	Stomach Mucosa	stomach
5	chr20:52631400-52637000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:52631400-52641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr20:52631600-52634600	Weak transcription	Fetal Lung	lung
8	chr20:52631600-52636000	Weak transcription	NHDF-Ad	bronchial
9	chr20:52632000-52635000	Enhancers	Brain Hippocampus Middle	brain
10	chr20:52633000-52634000	Enhancers	Brain Anterior Caudate	brain
11	chr20:52633000-52635000	Enhancers	Primary B cells from cord blood	blood
12	chr20:52633000-52635400	Enhancers	Primary B cells from peripheral blood	blood
13	chr20:52633000-52636000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr20:52633200-52633800	Enhancers	Brain Angular Gyrus	brain
15	chr20:52633200-52633800	Enhancers	Brain Cingulate Gyrus	brain
16	chr20:52633200-52634800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:52633200-52634800	Enhancers	Brain Substantia Nigra	brain
18	chr20:52633400-52633800	Flanking Active TSS	GM12878-XiMat	blood
19	chr20:52633400-52634400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:52633400-52634400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr20:52633400-52635000	Enhancers	Adipose Nuclei	Adipose
22	chr20:52633400-52635000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr20:52633600-52633800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr20:52633600-52634400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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