Variant report

Variant	rs2059794
Chromosome Location	chr5:79333415-79333416
allele	A/C
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	NFIC	chr5:79333119-79333699	GM12878	blood:	n/a	n/a
2	RUNX3	chr5:79333235-79333629	GM12878	blood:	n/a	n/a
3	RUNX3	chr5:79333166-79333652	GM12878	blood:	n/a	n/a
4	IKZF1	chr5:79333373-79333672	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79332099..79334519-chr5:79339709..79341668,2	K562	blood:

Variant related genes	Relation type
TRMT112P2	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10474605	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1438735	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1438736	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1438737	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs166270	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118731	0.93[EUR][1000 genomes]
rs2241825	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249687	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2249794	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2434277	0.91[CEU][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2434278	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2434280	0.81[EUR][1000 genomes]
rs2434282	0.80[EUR][1000 genomes]
rs2434299	0.85[EUR][1000 genomes]
rs2434301	0.86[EUR][1000 genomes]
rs2434302	0.92[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2434303	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2434304	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2434312	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2434320	0.93[EUR][1000 genomes]
rs2438645	0.85[EUR][1000 genomes]
rs2438649	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451932	0.87[EUR][1000 genomes]
rs256442	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256443	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs256445	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2913544	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2918422	0.83[EUR][1000 genomes]
rs364988	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs368287	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs368936	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs380747	0.90[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs382746	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384941	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs394947	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs397601	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs404375	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs405112	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs407314	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs411240	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs411943	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs412379	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs426623	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs428279	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs432267	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6861685	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs689879	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs690284	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690325	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692979	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs693270	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7446065	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv882219	chr5:79320677-79354147	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882220	chr5:79321439-79335975	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv882221	chr5:79321439-79350726	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv882222	chr5:79321439-79354147	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv598743	chr5:79329538-79335267	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv882223	chr5:79330559-79357117	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79331800-79335200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:79332000-79337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:79332200-79335600	Weak transcription	Brain Substantia Nigra	brain
4	chr5:79332200-79337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:79332600-79336800	Weak transcription	Brain Angular Gyrus	brain
6	chr5:79332800-79333800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:79332800-79333800	Active TSS	Fetal Muscle Leg	muscle
8	chr5:79332800-79336800	Weak transcription	Brain Anterior Caudate	brain
9	chr5:79332800-79339200	Weak transcription	Left Ventricle	heart
10	chr5:79332800-79350200	Weak transcription	Fetal Muscle Trunk	muscle

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