Variant report

Variant	rs2054905
Chromosome Location	chr12:48687951-48687952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48677853..48680154-chr12:48686621..48688237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258234	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1061986	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875743	1.00[CHB][hapmap]
rs10875749	1.00[CHB][hapmap]
rs10875753	1.00[CHB][hapmap]
rs10875763	0.83[ASN][1000 genomes]
rs1107654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168408	1.00[CHB][hapmap]
rs11168428	1.00[CHB][hapmap]
rs11168437	1.00[CHB][hapmap]
rs11168441	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168464	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168468	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168474	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168484	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228750	1.00[CHB][hapmap]
rs12368659	1.00[CHB][hapmap]
rs12816820	1.00[CHB][hapmap]
rs12828309	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829841	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387259	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1387260	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1476607	1.00[CHB][hapmap]
rs1489108	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1542707	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552550	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601985	0.81[AMR][1000 genomes]
rs2409003	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2409004	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2450994	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2450996	0.83[EUR][1000 genomes]
rs2468943	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2468949	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2634670	0.82[AMR][1000 genomes]
rs2634676	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2634678	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2634680	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2634681	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2634682	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2634684	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2634686	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2634688	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2634689	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2634691	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634692	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634693	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634694	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2634697	1.00[ASN][1000 genomes]
rs2732441	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732445	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2732448	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732453	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732454	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732457	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2732461	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2732462	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2732466	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2732479	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732481	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732484	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732486	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732488	0.81[AMR][1000 genomes]
rs2956703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2956710	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087716	0.83[ASN][1000 genomes]
rs34286639	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580662	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301003	1.00[CHB][hapmap]
rs7307566	1.00[CHB][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486941	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7487682	1.00[CHB][hapmap]
rs7959684	1.00[CHB][hapmap]
rs7966829	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8716	1.00[CHB][hapmap]
rs923397	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs973398	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv899062	chr12:48658212-48711867	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv899063	chr12:48664989-48713768	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	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
9	nsv899065	chr12:48667019-48711867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv899066	chr12:48667019-48713768	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	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
12	esv34952	chr12:48672333-48703533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv469369	chr12:48675783-48711867	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv469370	chr12:48675783-48711867	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv469372	chr12:48675783-48711867	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv470290	chr12:48675783-48711867	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv558791	chr12:48675783-48711867	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2054905	H1FNT	cis	Muscle Skeletal	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48686000-48690800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48686800-48690200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:48687200-48690200	Enhancers	Primary neutrophils fromperipheralblood	blood

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