Variant report

Variant	rs2408954
Chromosome Location	chr12:48422489-48422490
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	NR2F2	chr12:48422206-48422854	MCF-7	breast:	n/a	n/a
2	POLR2A	chr12:48422065-48422638	K562	blood:	n/a	n/a
3	MAX	chr12:48422259-48422921	MCF-7	breast:	n/a	chr12:48422695-48422705 chr12:48422747-48422754 chr12:48422694-48422703
4	ZNF384	chr12:48422321-48422678	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48421385..48423662-chr12:48427630..48429692,2	K562	blood:
2	chr12:48359708..48361971-chr12:48421078..48422974,2	MCF-7	breast:
3	chr12:48415815..48418237-chr12:48421031..48422834,2	K562	blood:
4	chr12:48421744..48425259-chr12:48425932..48429243,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257955	TF binding region
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10450783	0.86[EUR][1000 genomes]
rs10492082	0.95[ASN][1000 genomes]
rs1049392	1.00[JPT][hapmap]
rs10747529	1.00[JPT][hapmap]
rs10875726	0.90[ASN][1000 genomes]
rs10875727	0.90[ASN][1000 genomes]
rs10875733	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875739	1.00[JPT][hapmap]
rs10875752	1.00[JPT][hapmap]
rs10875754	1.00[JPT][hapmap]
rs10875761	1.00[JPT][hapmap]
rs10875766	1.00[JPT][hapmap]
rs11168350	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11168353	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168354	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168358	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168361	0.96[ASN][1000 genomes]
rs11168363	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11168364	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11168373	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168404	1.00[JPT][hapmap]
rs11168417	1.00[JPT][hapmap]
rs11168424	1.00[JPT][hapmap]
rs11168434	1.00[JPT][hapmap]
rs11168435	1.00[JPT][hapmap]
rs11168438	1.00[JPT][hapmap]
rs11168445	1.00[JPT][hapmap]
rs11168448	1.00[JPT][hapmap]
rs11168453	1.00[JPT][hapmap]
rs11168454	1.00[JPT][hapmap]
rs11834818	0.82[ASN][1000 genomes]
rs12422355	1.00[JPT][hapmap]
rs12423250	0.94[JPT][hapmap]
rs12426981	0.82[ASN][1000 genomes]
rs17122567	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1859440	0.91[ASN][1000 genomes]
rs1859442	0.85[ASN][1000 genomes]
rs1859443	0.94[JPT][hapmap]
rs1978161	0.82[JPT][hapmap]
rs2056448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240306	0.92[ASN][1000 genomes]
rs2286020	1.00[JPT][hapmap]
rs3742075	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3825403	1.00[JPT][hapmap]
rs4258439	1.00[JPT][hapmap]
rs58086963	0.85[ASN][1000 genomes]
rs59667534	0.95[ASN][1000 genomes]
rs6580658	0.82[JPT][hapmap]
rs7134203	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs7134878	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7299704	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7302354	1.00[JPT][hapmap]
rs7303677	1.00[JPT][hapmap]
rs733592	0.91[ASN][1000 genomes]
rs7484942	1.00[JPT][hapmap]
rs765260	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7962390	1.00[JPT][hapmap]
rs7962569	0.94[JPT][hapmap]
rs8181670	1.00[JPT][hapmap]
rs886589	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs954326	0.94[JPT][hapmap]
rs9651981	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9804751	0.94[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48416800-48423400	Weak transcription	Right Atrium	heart
2	chr12:48417800-48423400	Weak transcription	Fetal Lung	lung
3	chr12:48418200-48424200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48418400-48425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:48418600-48425200	Enhancers	Fetal Intestine Large	intestine
6	chr12:48420000-48424200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:48420200-48422800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48420200-48423800	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:48420200-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:48420400-48424000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:48420400-48424000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:48420400-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:48420400-48429000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:48420600-48424200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:48420800-48424600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:48421400-48422800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr12:48421400-48425000	Enhancers	Fetal Intestine Small	intestine
18	chr12:48421600-48423800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:48421600-48425000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:48421800-48422600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:48421800-48423400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:48421800-48423800	Enhancers	HepG2	liver
23	chr12:48421800-48424000	Weak transcription	HMEC	breast
24	chr12:48422000-48424400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:48422000-48429000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:48422200-48423200	Enhancers	Primary B cells from peripheral blood	blood
27	chr12:48422200-48424000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr12:48422200-48424400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:48422200-48424800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr12:48422200-48425000	Enhancers	Fetal Heart	heart
31	chr12:48422400-48422600	Enhancers	Colon Smooth Muscle	Colon
32	chr12:48422400-48422600	Enhancers	Psoas Muscle	Psoas
33	chr12:48422400-48422600	Enhancers	Right Ventricle	heart
34	chr12:48422400-48422800	Enhancers	Fetal Kidney	kidney
35	chr12:48422400-48424200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr12:48422400-48424800	Enhancers	K562	blood

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