Variant report

Variant	rs6083449
Chromosome Location	chr20:24216942-24216943
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	CTCF	chr20:24216900-24217050	GM12869	blood:	n/a	n/a

Variant related genes	Relation type
RNU1-23P	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12373871	1.00[ASN][1000 genomes]
rs28778436	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282312	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282314	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282316	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55739770	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55771985	0.83[EUR][1000 genomes]
rs56104572	0.96[EUR][1000 genomes]
rs59054030	0.96[EUR][1000 genomes]
rs59561448	0.96[EUR][1000 genomes]
rs6049548	0.90[EUR][1000 genomes]
rs6049554	0.93[EUR][1000 genomes]
rs6049555	0.96[EUR][1000 genomes]
rs6049556	0.96[EUR][1000 genomes]
rs6076190	0.83[EUR][1000 genomes]
rs6076194	0.83[EUR][1000 genomes]
rs6076195	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076200	1.00[ASN][1000 genomes]
rs6076205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6076206	1.00[ASN][1000 genomes]
rs6076214	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6076217	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6083388	0.83[EUR][1000 genomes]
rs6083390	0.83[EUR][1000 genomes]
rs6083391	0.83[EUR][1000 genomes]
rs6083398	0.83[EUR][1000 genomes]
rs6083400	0.83[EUR][1000 genomes]
rs6083404	0.86[EUR][1000 genomes]
rs6083406	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083408	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083409	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083424	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083432	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083433	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083436	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083439	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083440	1.00[ASN][1000 genomes]
rs6083441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6083463	0.96[EUR][1000 genomes]
rs6083464	0.96[EUR][1000 genomes]
rs6083465	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6083467	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6083473	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6083480	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6083484	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6083486	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6083487	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6083488	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6106813	0.96[EUR][1000 genomes]
rs73329997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73333779	0.96[EUR][1000 genomes]
rs73335617	0.96[EUR][1000 genomes]
rs73337581	1.00[ASN][1000 genomes]
rs7354351	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962527	0.89[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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3328348	chr20:24095746-24285830	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv833945	chr20:24163437-24349462	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24215600-24217200	Enhancers	Brain Substantia Nigra	brain
2	chr20:24215800-24217000	Enhancers	Brain Cingulate Gyrus	brain
3	chr20:24215800-24217200	Enhancers	Brain Germinal Matrix	brain
4	chr20:24215800-24217200	Enhancers	Brain Hippocampus Middle	brain
5	chr20:24215800-24217200	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr20:24215800-24217600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:24215800-24217800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr20:24216000-24217000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr20:24216000-24217000	Weak transcription	Fetal Muscle Leg	muscle
10	chr20:24216000-24217200	Enhancers	Brain Angular Gyrus	brain
11	chr20:24216000-24217200	Enhancers	Fetal Stomach	stomach
12	chr20:24216000-24217800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:24216800-24217200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr20:24216800-24217200	Enhancers	Liver	Liver
15	chr20:24216800-24217200	Enhancers	Brain Anterior Caudate	brain
16	chr20:24216800-24217400	Enhancers	Fetal Muscle Trunk	muscle

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