Variant report

Variant	rs6022904
Chromosome Location	chr20:52613382-52613383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:52613317-52613407	Hela-S3	cervix:	n/a	n/a
2	MAFK	chr20:52613306-52614096	GM12878	blood:	n/a	chr20:52613677-52613692
3	MAX	chr20:52613315-52613482	NB4	blood:	n/a	chr20:52613426-52613436
4	REST	chr20:52613018-52616478	MCF-7	breast:	n/a	n/a
5	MAFK	chr20:52613298-52613870	IMR90	lung:	n/a	chr20:52613677-52613692
6	TEAD4	chr20:52612977-52614148	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:56707941..56710505-chr20:52611192..52614067,2	MCF-7	breast:
2	chr17:56735310..56737024-chr20:52612265..52614955,3	MCF-7	breast:
3	chr20:52612843..52613434-chr3:64020702..64021214,2	MCF-7	breast:

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs6013858	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6013859	0.95[EUR][1000 genomes]
rs6013860	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6013862	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6013863	0.95[EUR][1000 genomes]
rs6013864	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6013865	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6013866	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6013867	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022891	0.89[AFR][1000 genomes]
rs6022892	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022893	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022894	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6022895	0.95[EUR][1000 genomes]
rs6022896	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022897	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022899	0.95[EUR][1000 genomes]
rs6022903	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022905	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022906	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022907	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022908	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022909	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022910	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6022911	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6097705	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7274783	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs740049	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs878868	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs881206	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv11894	chr20:52613366-52614476	Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 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	chr20:52604400-52618200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52612200-52614400	Enhancers	Brain Hippocampus Middle	brain
5	chr20:52612200-52614600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr20:52612200-52614800	Enhancers	Brain Substantia Nigra	brain
7	chr20:52612400-52613400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr20:52612400-52613600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:52612400-52614400	Enhancers	Brain Anterior Caudate	brain
10	chr20:52612400-52614600	Enhancers	Brain Cingulate Gyrus	brain
11	chr20:52612600-52618600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr20:52613000-52614400	Enhancers	Brain Angular Gyrus	brain
13	chr20:52613200-52613600	Enhancers	HSMMtube	muscle

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