Variant report

Variant	rs1264239
Chromosome Location	chr12:65075817-65075818
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65004483..65006802-chr12:65074574..65078170,3	MCF-7	breast:
2	chr12:65064246..65067121-chr12:65074124..65076207,3	K562	blood:
3	chr12:65001939..65003947-chr12:65074354..65078744,4	MCF-7	breast:
4	chr12:65040502..65042059-chr12:65074229..65075840,2	MCF-7	breast:
5	chr12:65018029..65021346-chr12:65072247..65076410,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256670	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10748011	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11175496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1147097	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1147104	0.86[EUR][1000 genomes]
rs1147106	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1244870	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1244871	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1244872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1244881	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1245170	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1261879	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1270430	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690261	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716495	0.82[AMR][1000 genomes]
rs1716497	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1716518	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1795614	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1795617	0.82[EUR][1000 genomes]
rs1797690	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1797699	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682713	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2682717	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2682721	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4264239	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572046	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577303	0.91[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307999	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7308397	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
4	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS 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	15 gene(s)	inside rSNPs	diseases
6	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65064000-65076000	Enhancers	Fetal Thymus	thymus
2	chr12:65064000-65078200	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:65066000-65078600	Enhancers	Spleen	Spleen
4	chr12:65067400-65076800	Weak transcription	Brain Angular Gyrus	brain
5	chr12:65068000-65076800	Weak transcription	Brain Germinal Matrix	brain
6	chr12:65068400-65087200	Weak transcription	Liver	Liver
7	chr12:65068600-65076600	Weak transcription	Fetal Kidney	kidney
8	chr12:65068600-65076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:65068600-65078000	Weak transcription	Dnd41	blood
10	chr12:65068600-65079400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:65069400-65077000	Weak transcription	Psoas Muscle	Psoas
12	chr12:65070000-65085200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:65070000-65092400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:65070600-65076600	Enhancers	Fetal Heart	heart
15	chr12:65070800-65076000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:65070800-65079600	Enhancers	Colon Smooth Muscle	Colon
17	chr12:65072000-65077400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:65072200-65077200	Enhancers	Left Ventricle	heart
19	chr12:65072200-65081600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:65072400-65076000	Enhancers	Stomach Mucosa	stomach
21	chr12:65072600-65076400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:65072600-65078400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:65072800-65076400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:65073200-65076000	Genic enhancers	GM12878-XiMat	blood
25	chr12:65073200-65078400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr12:65073400-65078000	Enhancers	Fetal Stomach	stomach
27	chr12:65073600-65076000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:65073600-65076000	Enhancers	HepG2	liver
29	chr12:65073600-65077600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr12:65073800-65076000	Enhancers	Small Intestine	intestine
31	chr12:65073800-65076400	Weak transcription	NHLF	lung
32	chr12:65073800-65077400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:65073800-65077400	Weak transcription	Fetal Brain Male	brain
34	chr12:65073800-65077400	Enhancers	K562	blood
35	chr12:65074000-65076400	Weak transcription	NHDF-Ad	bronchial
36	chr12:65074000-65076600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:65074000-65077000	Enhancers	HUVEC	blood vessel
38	chr12:65074000-65078000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr12:65074000-65079000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:65074000-65081600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:65074200-65076400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:65074200-65076600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr12:65074200-65076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:65074200-65076600	Enhancers	Stomach Smooth Muscle	stomach
45	chr12:65074200-65077000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:65074200-65078600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:65074200-65079000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:65074200-65079000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr12:65074200-65079000	Weak transcription	Colonic Mucosa	Colon
50	chr12:65074200-65081400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links