Variant report

Variant	rs56273568
Chromosome Location	chr12:57612541-57612542
allele	A/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	FOXA2	chr12:57612399-57612689	HepG2	liver:	n/a	n/a
2	FOXA1	chr12:57612275-57612758	T-47D	breast:	n/a	chr12:57612547-57612562
3	FOXA1	chr12:57612351-57612706	T-47D	breast:	n/a	chr12:57612547-57612562
4	SUZ12	chr12:57612382-57613243	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF263	chr12:57612355-57613231	HEK293-T-REx	kidney:	n/a	n/a
6	FOXP2	chr12:57612230-57612715	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57609766..57611384-chr12:57611404..57613261,2	MCF-7	breast:
2	chr12:57552323..57555013-chr12:57611507..57613175,2	MCF-7	breast:
3	chr12:57608303..57611284-chr12:57611816..57613934,2	MCF-7	breast:

Variant related genes	Relation type
NXPH4	TF binding region
ENSG00000182379	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11172219	1.00[EUR][1000 genomes]
rs11557166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17854829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28365863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34248177	1.00[EUR][1000 genomes]
rs34343116	0.80[ASN][1000 genomes]
rs34950222	1.00[EUR][1000 genomes]
rs35021926	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61978619	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62620661	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7304504	1.00[EUR][1000 genomes]
rs74093103	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74093104	1.00[EUR][1000 genomes]
rs74093113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74093115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74093117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv869636	chr12:57590172-57613714	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57609800-57614600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:57611200-57613800	Bivalent Enhancer	Fetal Heart	heart
3	chr12:57611400-57612600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr12:57611400-57613600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:57611400-57614600	Bivalent Enhancer	Fetal Lung	lung
6	chr12:57611400-57614600	Bivalent Enhancer	Fetal Stomach	stomach
7	chr12:57611400-57615400	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr12:57611400-57623000	Weak transcription	Right Atrium	heart
9	chr12:57611600-57612600	Bivalent Enhancer	Primary B cells from cord blood	blood
10	chr12:57611600-57612800	Bivalent Enhancer	Placenta	Placenta
11	chr12:57611600-57612800	Enhancers	A549	lung
12	chr12:57611600-57613000	Bivalent Enhancer	NHLF	lung
13	chr12:57611600-57613800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:57611800-57612600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:57611800-57612600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:57611800-57612800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:57611800-57613000	Bivalent Enhancer	Brain Germinal Matrix	brain
18	chr12:57611800-57613000	Bivalent Enhancer	NHEK	skin
19	chr12:57611800-57613600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:57611800-57614200	Weak transcription	Right Ventricle	heart
21	chr12:57611800-57615600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr12:57611800-57618400	Weak transcription	Pancreas	Pancrea
23	chr12:57612000-57613000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:57612000-57614400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:57612200-57613200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr12:57612400-57612600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
27	chr12:57612400-57612600	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
28	chr12:57612400-57613000	Flanking Active TSS	Fetal Brain Female	brain

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