Variant report

Variant	rs765260
Chromosome Location	chr12:48431936-48431937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48426470..48428398-chr12:48428806..48432334,3	MCF-7	breast:
2	chr12:48377455..48379308-chr12:48429831..48432694,2	K562	blood:
3	chr12:48426621..48428717-chr12:48430919..48432434,2	K562	blood:
4	chr12:48422786..48426072-chr12:48430482..48433177,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10492082	0.92[ASN][1000 genomes]
rs1049392	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10747529	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10875726	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875727	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875733	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875739	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap]
rs10875752	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10875754	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10875761	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10875766	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11168350	0.94[JPT][hapmap]
rs11168353	1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168361	0.89[ASN][1000 genomes]
rs11168363	0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168364	0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168373	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168404	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11168417	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11168424	1.00[JPT][hapmap]
rs11168434	1.00[JPT][hapmap]
rs11168435	0.82[CHD][hapmap];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	0.81[ASN][1000 genomes]
rs12422355	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12423250	0.94[JPT][hapmap]
rs12426981	0.81[ASN][1000 genomes]
rs17122567	1.00[JPT][hapmap]
rs1859440	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859443	0.94[JPT][hapmap]
rs1978161	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2056448	0.89[ASN][1000 genomes]
rs2107640	0.87[EUR][1000 genomes]
rs2240306	0.91[ASN][1000 genomes]
rs2286020	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2408954	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3742075	0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs3825403	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs4258439	0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[ASN][1000 genomes]
rs4760678	0.88[EUR][1000 genomes]
rs59667534	0.92[ASN][1000 genomes]
rs6580658	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7138917	0.86[ASN][1000 genomes]
rs7299704	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7302354	1.00[JPT][hapmap]
rs7303677	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs733592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484942	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7962390	1.00[JPT][hapmap]
rs7962569	0.94[JPT][hapmap]
rs8181670	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs886589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs954326	0.94[JPT][hapmap]
rs9651981	0.94[JPT][hapmap]
rs9804751	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	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
3	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs765260	PFKM	cis	parietal	SCAN
rs765260	SENP1	cis	parietal	SCAN
rs765260	RP1-228P16.1	cis	Artery Tibial	GTEx
rs765260	RP1-228P16.1	cis	Thyroid	GTEx
rs765260	LOC255411	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:48424800-48437400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:48427600-48435600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:48428600-48432200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:48429000-48434200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:48429200-48433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:48429200-48437000	Weak transcription	GM12878-XiMat	blood
8	chr12:48429400-48433200	Weak transcription	Colonic Mucosa	Colon
9	chr12:48429400-48435400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:48429600-48436400	Weak transcription	HMEC	breast
11	chr12:48429800-48434200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:48430200-48432000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48430200-48433200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:48430400-48432200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr12:48430600-48432000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:48430600-48432000	Enhancers	Fetal Intestine Small	intestine
17	chr12:48430600-48432000	Enhancers	Fetal Kidney	kidney
18	chr12:48430600-48432000	Enhancers	Fetal Lung	lung
19	chr12:48430600-48432000	Enhancers	Ovary	ovary
20	chr12:48430600-48432000	Enhancers	Right Ventricle	heart
21	chr12:48430600-48432200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:48430600-48432200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:48430600-48432200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:48430600-48432200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:48430600-48432400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:48430800-48432000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:48430800-48432000	Enhancers	Fetal Thymus	thymus
28	chr12:48430800-48432800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:48431000-48432000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr12:48431000-48432000	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:48431000-48432000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr12:48431000-48432000	Enhancers	Fetal Heart	heart
33	chr12:48431000-48432000	Enhancers	Spleen	Spleen
34	chr12:48431000-48432000	Enhancers	HSMM	muscle
35	chr12:48431000-48432200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:48431000-48432200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:48431000-48432200	Flanking Active TSS	HepG2	liver
38	chr12:48431000-48432400	Enhancers	Fetal Intestine Large	intestine
39	chr12:48431200-48432000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:48431200-48432000	Enhancers	NHDF-Ad	bronchial
41	chr12:48431200-48433200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:48431400-48432000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:48431400-48432000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
44	chr12:48431400-48436600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr12:48431400-48438200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:48431400-48438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:48431600-48432000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
48	chr12:48431600-48432000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
49	chr12:48431600-48432000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr12:48431600-48432200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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