Variant report

Variant	rs2299699
Chromosome Location	chr20:52665778-52665779
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:59805932..59807613-chr20:52665362..52667872,2	MCF-7	breast:
2	chr20:52637587..52640113-chr20:52663021..52665849,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11905945	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1381983	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1381984	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1557853	0.87[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072128	0.87[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2107327	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2189502	0.84[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2214530	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2238701	0.85[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2276487	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276488	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276489	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276491	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2299698	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299701	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299702	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299704	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2299705	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299707	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299711	0.87[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2299712	0.87[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299715	0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299718	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2870304	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34973146	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35883829	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6091807	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6091808	0.87[JPT][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs6091811	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6091812	0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6097745	0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6097749	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6123344	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6123345	0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6127058	0.93[EUR][1000 genomes]
rs6127060	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6127061	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6127062	0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6127063	0.88[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6127065	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6127066	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6127068	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6127072	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6127073	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67082409	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71323984	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73133436	0.92[EUR][1000 genomes]
rs732344	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs765348	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
5	nsv1055891	chr20:52647808-52666885	Enhancers Strong transcription Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv1067336	chr20:52647808-52668126	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv1065888	chr20:52647808-52670378	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv586250	chr20:52647823-52671132	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv1055306	chr20:52651154-52666885	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:52664800-52666000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr20:52664800-52666000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:52664800-52666000	Enhancers	NHDF-Ad	bronchial
8	chr20:52665000-52665800	Enhancers	NHLF	lung
9	chr20:52665400-52666400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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