Variant report

Variant	rs12645402
Chromosome Location	chr4:54525329-54525330
allele	C/G
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	EP300	chr4:54525216-54525671	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr4:54525280-54525675	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr4:54525318-54525730	SK-N-SH_RA	brain:	n/a	n/a
4	TCF12	chr4:54525285-54525776	SK-N-SH	brain:	n/a	n/a
5	EP300	chr4:54525239-54525677	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000249341	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10005578	0.83[ASN][1000 genomes]
rs10006267	0.83[ASN][1000 genomes]
rs10010205	0.83[ASN][1000 genomes]
rs10021678	0.81[ASN][1000 genomes]
rs10027185	0.88[ASN][1000 genomes]
rs10027544	0.87[ASN][1000 genomes]
rs10031525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031866	0.82[ASN][1000 genomes]
rs1039985	0.94[ASN][1000 genomes]
rs13146347	0.88[ASN][1000 genomes]
rs13148245	0.83[ASN][1000 genomes]
rs1477878	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1477880	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17083218	0.83[ASN][1000 genomes]
rs17083272	0.93[ASN][1000 genomes]
rs17083277	0.92[ASN][1000 genomes]
rs1991972	0.88[ASN][1000 genomes]
rs1991973	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2086048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2219742	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28678201	0.80[ASN][1000 genomes]
rs3942650	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864809	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554120	0.89[ASN][1000 genomes]
rs6554121	0.88[ASN][1000 genomes]
rs6816209	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6818959	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6822736	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6843799	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858782	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs750695	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7688605	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54522200-54526000	Weak transcription	Gastric	stomach
2	chr4:54522200-54526000	Weak transcription	Right Atrium	heart
3	chr4:54522400-54525400	Weak transcription	Stomach Mucosa	stomach
4	chr4:54523400-54525400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:54524000-54526600	Enhancers	Fetal Heart	heart
6	chr4:54524200-54525800	Enhancers	Fetal Stomach	stomach
7	chr4:54524200-54526200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:54524200-54526400	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links