Variant report

Variant	rs6123333
Chromosome Location	chr20:52578849-52578850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:732113..733855-chr20:52577889..52580528,2	MCF-7	breast:
2	chr17:55980748..55982351-chr20:52577090..52579226,2	MCF-7	breast:
3	chr20:52578439..52580096-chr4:70380828..70382348,2	MCF-7	breast:
4	chr20:52572078..52574056-chr20:52577646..52580045,2	K562	blood:
5	chr20:52578676..52580952-chr20:52822613..52824922,2	MCF-7	breast:
6	chr17:59938997..59940771-chr20:52578844..52581418,2	MCF-7	breast:
7	chr20:52578607..52581315-chr8:144821296..144823256,2	MCF-7	breast:
8	chr20:52576980..52579771-chr20:52581907..52583862,2	K562	blood:
9	chr20:52577489..52580206-chr6:39156376..39158164,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000203499	Chromatin interaction
ENSG00000180891	Chromatin interaction
ENSG00000161999	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000103266	Chromatin interaction
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs208382	1.00[CEU][hapmap]
rs2276495	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs2276505	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs2299732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2302040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6123334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6127036	0.91[ASN][1000 genomes]
rs73622290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73622291	1.00[AMR][1000 genomes];0.88[EUR][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	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	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
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52567000-52580200	Weak transcription	Stomach Mucosa	stomach
3	chr20:52570200-52591800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr20:52570800-52590800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:52576400-52591400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr20:52576800-52579200	Enhancers	NHDF-Ad	bronchial
8	chr20:52577000-52580400	Weak transcription	Fetal Muscle Leg	muscle
9	chr20:52578400-52580200	Weak transcription	Fetal Stomach	stomach
10	chr20:52578400-52591200	Weak transcription	HSMMtube	muscle
11	chr20:52578600-52580400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr20:52578600-52592400	Weak transcription	Brain Hippocampus Middle	brain
13	chr20:52578800-52591800	Weak transcription	Brain Anterior Caudate	brain
14	chr20:52578800-52592400	Weak transcription	Brain Substantia Nigra	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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