Variant report

Variant	rs2634688
Chromosome Location	chr12:48719536-48719537
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	POLR2A	chr12:48719444-48719635	MCF-7	breast:	n/a	n/a
2	FOXA2	chr12:48719246-48719823	A549	lung:	n/a	n/a
3	POLR2A	chr12:48719521-48719627	MCF-7	breast:	n/a	n/a
4	SETDB1	chr12:48719512-48719966	U2OS	brain:	n/a	n/a
5	FOXA2	chr12:48719364-48719765	A549	lung:	n/a	n/a
6	FOXA1	chr12:48719385-48719769	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48718530..48720177-chr12:48742678..48744445,2	MCF-7	breast:

Variant related genes	Relation type
H1FNT	TF binding region
ENSG00000167528	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1061986	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1107654	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168468	0.83[EUR][1000 genomes]
rs11168474	0.82[EUR][1000 genomes]
rs11168484	0.85[EUR][1000 genomes]
rs12828309	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12829841	0.85[EUR][1000 genomes]
rs1387259	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1387260	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1489108	0.88[EUR][1000 genomes]
rs1542707	0.85[EUR][1000 genomes]
rs1552550	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2054905	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2409003	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409004	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450994	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450996	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2468943	0.85[EUR][1000 genomes]
rs2468946	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2468949	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634676	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2634678	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2634680	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2634681	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634682	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634684	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2634686	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634689	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634691	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634692	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634693	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634694	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732441	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732448	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732453	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732454	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732457	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2732461	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2732462	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2732466	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2732479	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732480	0.83[ASN][1000 genomes]
rs2732481	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732484	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732486	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2956703	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2956710	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34286639	0.85[EUR][1000 genomes]
rs6580662	0.83[EUR][1000 genomes]
rs7307566	0.82[EUR][1000 genomes]
rs7966829	0.82[EUR][1000 genomes]
rs923397	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	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
8	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2634688	H1FNT	cis	Muscle Skeletal	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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