Variant report

Variant	rs2299715
Chromosome Location	chr20:52639242-52639243
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52636698..52639265-chr20:52824391..52826497,2	MCF-7	breast:
2	chr20:52637571..52639350-chr20:52639396..52641959,2	K562	blood:
3	chr20:52637587..52640113-chr20:52663021..52665849,2	MCF-7	breast:
4	chr20:52638922..52641694-chr20:52671102..52673075,2	MCF-7	breast:
5	chr20:52637408..52640155-chr20:52655059..52656752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11905945	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1381983	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1381984	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1557853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107327	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2189502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2214530	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238701	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2276487	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276488	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276489	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276491	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2299698	0.92[EUR][1000 genomes]
rs2299699	0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299701	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299702	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299704	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs2299705	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299707	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299718	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2870304	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34973146	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35883829	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6091807	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6091808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6091811	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6091812	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6097749	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6123344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6123345	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127058	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127060	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127061	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127062	1.00[CEU][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127065	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6127066	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127068	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127072	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6127073	0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67082409	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71323984	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73133436	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs732344	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs765348	0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.88[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:12 , 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	chr20:52631400-52641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:52633800-52641200	Weak transcription	Brain Angular Gyrus	brain
5	chr20:52634800-52645400	Weak transcription	Fetal Lung	lung
6	chr20:52635800-52641800	Enhancers	Brain Substantia Nigra	brain
7	chr20:52636000-52641200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr20:52636600-52640600	Weak transcription	Stomach Mucosa	stomach
9	chr20:52637600-52640400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:52638800-52639400	Weak transcription	Brain Anterior Caudate	brain
11	chr20:52638800-52640000	Weak transcription	Brain Hippocampus Middle	brain
12	chr20:52639200-52640800	Weak transcription	Brain Cingulate Gyrus	brain

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