Variant report

Variant	rs6127058
Chromosome Location	chr20:52628804-52628805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52628442..52630921-chr20:52632411..52634269,2	K562	blood:
2	chr20:52118844..52121370-chr20:52626682..52629517,2	MCF-7	breast:
3	chr20:52628739..52630363-chr20:52636022..52638678,2	K562	blood:
4	chr1:150551110..150553692-chr20:52626582..52629121,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259723	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11905945	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1381983	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1381984	0.94[EUR][1000 genomes]
rs1557853	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[EUR][1000 genomes]
rs2072128	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2107327	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2189502	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2214530	0.94[EUR][1000 genomes]
rs2276487	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2276488	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276489	0.94[EUR][1000 genomes]
rs2276491	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299698	0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs2299699	0.93[EUR][1000 genomes]
rs2299701	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2299702	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2299704	1.00[CEU][hapmap]
rs2299705	0.94[EUR][1000 genomes]
rs2299707	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2299711	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2299712	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2299715	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2299717	0.90[ASN][1000 genomes]
rs2299718	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]
rs2870304	0.90[EUR][1000 genomes]
rs34973146	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35883829	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3819585	0.88[ASN][1000 genomes]
rs6091807	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6091808	0.81[EUR][1000 genomes]
rs6091811	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6091812	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6097749	0.90[EUR][1000 genomes]
rs6123345	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127060	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6127061	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127062	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127063	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127065	0.94[EUR][1000 genomes]
rs6127066	0.94[EUR][1000 genomes]
rs6127068	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6127072	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6127073	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67082409	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71323984	0.97[EUR][1000 genomes]
rs73133436	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs732344	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52601800-52630800	Weak transcription	Stomach Mucosa	stomach
3	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52619000-52630600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:52624000-52633400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr20:52624600-52630200	Weak transcription	Brain Anterior Caudate	brain
7	chr20:52626400-52630600	Weak transcription	Brain Hippocampus Middle	brain
8	chr20:52626800-52630000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:52627000-52630400	Weak transcription	Brain Substantia Nigra	brain
10	chr20:52627600-52633200	Weak transcription	Brain Angular Gyrus	brain
11	chr20:52628400-52631000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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