Variant report

Variant	rs1259426
Chromosome Location	chr12:31748381-31748382
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	chr12:31743328..31745615-chr12:31747440..31749216,2	MCF-7	breast:
2	chr12:31739424..31741927-chr12:31747863..31749994,2	K562	blood:

Variant related genes	Relation type
ENSG00000255867	Chromatin interaction
ENSG00000170456	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11051456	0.85[ASN][1000 genomes]
rs1150942	0.89[ASN][1000 genomes]
rs1150943	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150945	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150954	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150955	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150963	0.89[ASN][1000 genomes]
rs1259233	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259241	0.89[ASN][1000 genomes]
rs1259353	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259354	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259356	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259359	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259386	0.95[ASN][1000 genomes]
rs1259389	0.85[ASN][1000 genomes]
rs1259395	0.85[EUR][1000 genomes]
rs1259405	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259409	0.82[ASN][1000 genomes]
rs1259435	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259437	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259438	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259441	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1262390	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1272773	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1542536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1677173	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1677186	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1677187	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1677189	0.91[AMR][1000 genomes]
rs1677217	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1716194	0.85[ASN][1000 genomes]
rs1716210	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2061761	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568887	0.84[ASN][1000 genomes]
rs2604052	0.95[ASN][1000 genomes]
rs2617178	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2617191	0.82[ASN][1000 genomes]
rs2682671	0.84[ASN][1000 genomes]
rs2682674	0.82[ASN][1000 genomes]
rs2682677	0.82[ASN][1000 genomes]
rs2682679	0.82[ASN][1000 genomes]
rs2682695	0.84[ASN][1000 genomes]
rs4312145	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498080	0.81[EUR][1000 genomes]
rs793148	0.84[ASN][1000 genomes]
rs793149	0.84[ASN][1000 genomes]
rs793150	0.81[ASN][1000 genomes]
rs793173	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793174	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793175	0.86[ASN][1000 genomes]
rs793177	0.89[ASN][1000 genomes]
rs793186	0.82[ASN][1000 genomes]
rs899159	0.95[ASN][1000 genomes]
rs976874	0.88[EUR][1000 genomes];0.89[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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1804747	chr12:31743194-31748491	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1840310	chr12:31743194-31750986	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	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	chr12:31745000-31749800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:31745200-31750200	Weak transcription	Primary B cells from cord blood	blood
3	chr12:31745400-31750200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:31745400-31750400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:31745400-31760400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:31747000-31748400	Enhancers	HSMMtube	muscle
7	chr12:31747800-31748400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:31748000-31748800	Weak transcription	Fetal Heart	heart

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