Variant report

Variant	rs12578801
Chromosome Location	chr12:66555533-66555534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66548703..66551216-chr12:66555058..66558052,2	MCF-7	breast:
2	chr12:66550852..66561080-chr12:66561565..66565303,15	MCF-7	breast:
3	chr12:66554922..66556425-chr12:66697932..66699503,2	K562	blood:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10459263	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs10506479	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];1.00[AMR][1000 genomes]
rs10878379	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs10878380	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes]
rs10878384	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes]
rs10878387	1.00[AMR][1000 genomes]
rs10878388	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs11176044	0.93[AMR][1000 genomes]
rs11176046	1.00[AMR][1000 genomes]
rs11176047	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[AMR][1000 genomes]
rs11176048	1.00[AMR][1000 genomes]
rs11176050	1.00[AMR][1000 genomes]
rs11176051	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs11176058	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11176059	0.93[AMR][1000 genomes]
rs11176061	1.00[AMR][1000 genomes]
rs11176062	1.00[AMR][1000 genomes]
rs1152888	0.81[CHB][hapmap]
rs1168736	0.95[ASN][1000 genomes]
rs1168739	0.95[ASN][1000 genomes]
rs1168744	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs1168757	0.81[CHB][hapmap];0.82[GIH][hapmap]
rs1168758	0.80[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap]
rs1168772	0.80[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs1179914	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs12230221	1.00[AMR][1000 genomes]
rs12230240	1.00[AMR][1000 genomes]
rs12230800	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs12306484	0.89[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12423372	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs12578364	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578752	0.85[CEU][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578994	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12581033	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes]
rs12581836	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12582384	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes]
rs12814331	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12814606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12821415	0.92[AMR][1000 genomes]
rs12822410	1.00[AMR][1000 genomes]
rs12823414	0.81[ASN][1000 genomes]
rs12823732	1.00[AMR][1000 genomes]
rs12825992	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes]
rs1370129	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs1625441	0.89[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs17245364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732893	0.89[CEU][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17825931	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs17825943	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797410	0.94[ASN][1000 genomes]
rs1921080	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs1921082	0.89[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2701644	0.86[ASN][1000 genomes]
rs2701645	0.86[ASN][1000 genomes]
rs2701653	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs2701654	0.81[JPT][hapmap]
rs2701655	0.81[ASN][1000 genomes]
rs2870786	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[AMR][1000 genomes]
rs2904498	0.93[AMR][1000 genomes]
rs2917598	0.86[ASN][1000 genomes]
rs34406211	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34552143	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35131575	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35187440	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35447479	1.00[AMR][1000 genomes]
rs35971570	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36073795	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4281516	1.00[AMR][1000 genomes]
rs59112451	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60102429	1.00[AMR][1000 genomes]
rs66767092	1.00[AMR][1000 genomes]
rs71450848	1.00[AMR][1000 genomes]
rs737614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv541516	chr12:66547969-66596036	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv976636	chr12:66553474-66556236	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
4	chr12:66534600-66555600	Weak transcription	Small Intestine	intestine
5	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
6	chr12:66536400-66556200	Weak transcription	Right Ventricle	heart
7	chr12:66536400-66557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:66536400-66562400	Weak transcription	HMEC	breast
9	chr12:66536800-66556200	Weak transcription	Left Ventricle	heart
10	chr12:66537400-66556200	Weak transcription	Ovary	ovary
11	chr12:66538400-66556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:66538600-66560400	Weak transcription	Fetal Brain Male	brain
13	chr12:66539200-66558400	Weak transcription	A549	lung
14	chr12:66539400-66556200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:66539400-66561400	Weak transcription	Fetal Heart	heart
16	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:66544200-66557600	Weak transcription	K562	blood
19	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
20	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
21	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:66549200-66561800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:66549200-66561800	Weak transcription	Right Atrium	heart
24	chr12:66550000-66557600	Strong transcription	Primary T cells from cord blood	blood
25	chr12:66550200-66557400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:66550400-66559200	Weak transcription	Colonic Mucosa	Colon
27	chr12:66551200-66560400	Weak transcription	HepG2	liver
28	chr12:66551400-66558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:66552200-66556000	Strong transcription	Dnd41	blood
30	chr12:66552600-66555600	Strong transcription	Primary B cells from cord blood	blood
31	chr12:66552600-66556000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:66553000-66555800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:66553000-66555800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:66553000-66562200	Weak transcription	Brain Angular Gyrus	brain
35	chr12:66553200-66555600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:66553200-66556200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:66553200-66561600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:66553200-66562400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:66553400-66555800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:66553400-66559000	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:66553600-66555600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:66553600-66556600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:66553600-66557200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:66553800-66555600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:66553800-66557200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:66553800-66559200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:66553800-66561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:66554000-66555800	Weak transcription	Brain Substantia Nigra	brain
49	chr12:66554000-66555800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:66554000-66558600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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