Variant report

Variant	rs278152
Chromosome Location	chr12:120117279-120117280
allele	A/C
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	POLR2A	chr12:120116959-120121013	K562	blood:	n/a	n/a
2	POLR2A	chr12:120117172-120118184	U87	brain:	n/a	n/a
3	POLR2A	chr12:120116930-120117764	K562	blood:	n/a	n/a
4	POLR2A	chr12:120116799-120117942	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:120115889-120123052	K562	blood:	n/a	n/a
6	POLR2A	chr12:120117247-120118398	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:120117217-120118121	U87	brain:	n/a	n/a
8	POLR2A	chr12:120116315-120120167	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120105026..120107337-chr12:120115955..120117891,2	MCF-7	breast:
2	chr12:120105122..120114412-chr12:120115205..120125435,13	MCF-7	breast:

Variant related genes	Relation type
PRKAB1	TF binding region
ENSG00000248636	Chromatin interaction
ENSG00000111725	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10774503	0.88[CEU][hapmap]
rs10849688	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849690	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064873	0.83[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175878	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978107	0.83[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978108	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs202983	0.81[MEX][hapmap]
rs278102	0.81[MEX][hapmap]
rs278123	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278126	0.83[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs278143	1.00[CEU][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278144	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278145	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278147	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278148	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278151	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278154	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278155	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930004	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490266	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490267	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301592	0.88[CEU][hapmap]
rs7304996	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310266	0.83[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311779	0.88[CEU][hapmap]
rs7312321	0.88[CEU][hapmap]
rs7960723	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963248	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967558	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972600	0.83[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979627	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804667	0.83[CEU][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs278152	PXN	cis	cerebellum	SCAN
rs278152	WSB2	cis	cerebellum	SCAN
rs278152	COQ5	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120107400-120120400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:120107800-120119000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:120107800-120120200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:120107800-120120200	Strong transcription	Stomach Smooth Muscle	stomach
5	chr12:120107800-120120600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:120108000-120119600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:120108000-120120600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:120108200-120119800	Strong transcription	Fetal Thymus	thymus
9	chr12:120108200-120120200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:120108200-120120400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr12:120108200-120122000	Strong transcription	A549	lung
12	chr12:120108200-120161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:120108400-120120000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:120108400-120120000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:120108400-120120200	Strong transcription	Osteobl	bone
16	chr12:120108600-120120200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:120108600-120120200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:120108800-120118000	Strong transcription	Liver	Liver
19	chr12:120108800-120118200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:120108800-120119400	Strong transcription	NHEK	skin
21	chr12:120108800-120119800	Strong transcription	Hela-S3	cervix
22	chr12:120108800-120120200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:120108800-120120200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:120108800-120120800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:120109000-120119400	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr12:120109000-120120200	Strong transcription	Dnd41	blood
27	chr12:120109200-120120200	Strong transcription	Thymus	Thymus
28	chr12:120109200-120121200	Strong transcription	Fetal Stomach	stomach
29	chr12:120109400-120118400	Strong transcription	Fetal Kidney	kidney
30	chr12:120109400-120119000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:120109400-120119800	Strong transcription	Aorta	Aorta
32	chr12:120109400-120120000	Strong transcription	Fetal Brain Female	brain
33	chr12:120109400-120120200	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr12:120109400-120120200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:120109400-120120400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:120109400-120121200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:120109600-120118000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:120109600-120120400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:120110000-120119200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:120110000-120120200	Strong transcription	NHLF	lung
41	chr12:120110000-120120400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:120110000-120120400	Strong transcription	Brain Germinal Matrix	brain
43	chr12:120110200-120120200	Strong transcription	Pancreas	Pancrea
44	chr12:120110400-120120200	Strong transcription	NH-A	brain
45	chr12:120110600-120119600	Strong transcription	Colon Smooth Muscle	Colon
46	chr12:120110600-120120400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:120111000-120120400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:120111200-120120400	Strong transcription	HSMMtube	muscle
49	chr12:120111400-120119400	Strong transcription	K562	blood
50	chr12:120111600-120118000	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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