Variant report

Variant	rs61940777
Chromosome Location	chr12:48883947-48883948
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	RUNX3	chr12:48883878-48884459	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48875260..48877080-chr12:48883909..48886028,2	K562	blood:
2	chr12:48880500..48882865-chr12:48883478..48886344,3	K562	blood:
3	chr12:48882871..48884702-chr12:48885100..48887755,2	K562	blood:

Variant related genes	Relation type
C12orf54	TF binding region
ENSG00000177627	Chromatin interaction
ENSG00000240443	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11168613	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578360	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12579133	0.90[ASN][1000 genomes]
rs12580859	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581223	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12582586	0.82[EUR][1000 genomes]
rs12582594	0.82[EUR][1000 genomes]
rs17234937	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4397895	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426170	0.82[EUR][1000 genomes]
rs4547144	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55667337	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55685217	0.90[ASN][1000 genomes]
rs55971664	0.82[EUR][1000 genomes]
rs55983865	0.96[EUR][1000 genomes]
rs56034252	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56191575	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59337124	0.80[EUR][1000 genomes]
rs61940763	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940764	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61940766	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940767	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940768	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940776	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61940779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61940780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61940822	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942812	0.80[EUR][1000 genomes]
rs61942813	0.82[EUR][1000 genomes]
rs61942816	0.82[EUR][1000 genomes]
rs61942817	0.82[EUR][1000 genomes]
rs61942828	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61942829	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61942830	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61942831	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv975416	chr12:48882416-48893049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48881600-48884000	Enhancers	HMEC	breast
2	chr12:48882400-48884000	Enhancers	GM12878-XiMat	blood
3	chr12:48883200-48884000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:48883400-48884000	Enhancers	NHEK	skin
5	chr12:48883800-48885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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