Variant report

Variant	rs581978
Chromosome Location	chr19:39471471-39471472
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr19:39471136-39471888	U2OS	brain:	n/a	n/a
2	FOXA1	chr19:39471390-39471967	HepG2	liver:	n/a	n/a
3	CBX3	chr19:39471029-39471585	K562	blood:	n/a	n/a
4	CTCF	chr19:39471420-39471570	HepG2	liver:	n/a	n/a
5	RAD21	chr19:39471413-39471711	HepG2	liver:	n/a	n/a
6	FOXA1	chr19:39471425-39471866	HepG2	liver:	n/a	n/a
7	EP300	chr19:39471444-39471941	HepG2	liver:	n/a	n/a
8	CTCF	chr19:39471360-39471642	HepG2	liver:	n/a	n/a
9	TRIM28	chr19:39471116-39471519	K562	blood:	n/a	n/a
10	CBX3	chr19:39471188-39471531	K562	blood:	n/a	n/a
11	KAP1	chr19:39471274-39471633	U2OS	brain:	n/a	n/a
12	FOXA2	chr19:39471461-39471872	HepG2	liver:	n/a	n/a
13	KAP1	chr19:39470996-39471925	K562	blood:	n/a	n/a
14	CTCF	chr19:39471440-39471590	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:39420391..39423581-chr19:39468736..39471563,3	K562	blood:
2	chr19:39469273..39472050-chr19:39495885..39497816,2	MCF-7	breast:
3	chr19:39470454..39473191-chr19:39473840..39476726,2	MCF-7	breast:
4	chr19:39466590..39468490-chr19:39469783..39471749,2	MCF-7	breast:
5	chr19:39470241..39471919-chr19:39522742..39524502,2	MCF-7	breast:

No data

Variant related genes	Relation type
FBXO17	TF binding region
ENSG00000104835	Chromatin interaction
ENSG00000161243	Chromatin interaction
ENSG00000128626	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403486	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10408493	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415667	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12461981	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12608659	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654334	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1654336	0.86[YRI][hapmap]
rs17795157	0.92[YRI][hapmap]
rs2318464	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2318465	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2318956	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28378068	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34638406	0.81[ASN][1000 genomes]
rs3848622	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4801996	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs482342	0.92[YRI][hapmap]
rs483359	0.86[YRI][hapmap]
rs490761	0.85[EUR][1000 genomes]
rs55722117	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564474	0.86[YRI][hapmap]
rs57214361	0.93[EUR][1000 genomes]
rs57810919	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59268123	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs606372	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61265620	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs622528	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs637972	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs638015	0.89[EUR][1000 genomes]
rs649150	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs650027	0.95[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7249004	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7250349	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7251721	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7251820	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7258123	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258386	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72623864	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7508413	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8105165	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8105298	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3318111	chr19:39470551-39471952	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv3318109	chr19:39470601-39471926	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv3318112	chr19:39470626-39471892	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3318110	chr19:39470677-39471844	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3318113	chr19:39470691-39471842	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs581978	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs581978	FBXO27	cis	Esophagus Mucosa	GTEx
rs581978	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs581978	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39470200-39471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39470400-39472000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:39471200-39472000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:39471400-39471600	ZNF genes & repeats	Brain Hippocampus Middle	brain
5	chr19:39471400-39472000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
6	chr19:39471400-39472200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:39471400-39472200	Flanking Active TSS	HepG2	liver
8	chr19:39471400-39472800	Enhancers	Liver	Liver

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