Variant report

Variant	rs278145
Chromosome Location	chr12:120112099-120112100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120111898-120115572	K562	blood:	n/a	n/a
2	POLR2A	chr12:120111675-120112101	K562	blood:	n/a	n/a
3	POLR2A	chr12:120111892-120112240	K562	blood:	n/a	n/a
4	POLR2A	chr12:120111586-120112121	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120105122..120114412-chr12:120115205..120125435,13	MCF-7	breast:
2	chr12:120104335..120107623-chr12:120110345..120114528,7	MCF-7	breast:
3	chr12:120110278..120112130-chr12:120115411..120117269,3	MCF-7	breast:
4	chr12:120104750..120107660-chr12:120111377..120114502,3	MCF-7	breast:

No data

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

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10774503	0.88[CEU][hapmap]
rs10849688	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849690	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064849	0.81[AMR][1000 genomes]
rs11064873	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175878	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978107	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978108	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs202983	0.87[MEX][hapmap]
rs278102	0.87[MEX][hapmap]
rs278123	1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278126	0.83[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs278143	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278144	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278147	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278148	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278149	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278151	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278152	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]
rs278154	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278155	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930004	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4213	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490266	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490267	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301592	0.88[CEU][hapmap]
rs7304996	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310266	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311779	0.88[CEU][hapmap]
rs7312321	0.88[CEU][hapmap]
rs7960723	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963248	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967558	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972600	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979627	0.91[AMR][1000 genomes];0.92[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
rs278145	PXN	cis	cerebellum	SCAN
rs278145	WSB2	cis	cerebellum	SCAN
rs278145	COQ5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120106800-120116600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:120107400-120116400	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:120107400-120120400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:120107600-120112400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr12:120107600-120112600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:120107600-120116000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:120107600-120116200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:120107800-120112600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:120107800-120116400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:120107800-120116400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:120107800-120119000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:120107800-120120200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:120107800-120120200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr12:120107800-120120600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:120108000-120119600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:120108000-120120600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:120108200-120112200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:120108200-120113000	Strong transcription	HMEC	breast
19	chr12:120108200-120115800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:120108200-120119800	Strong transcription	Fetal Thymus	thymus
21	chr12:120108200-120120200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:120108200-120120400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:120108200-120122000	Strong transcription	A549	lung
24	chr12:120108200-120161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:120108400-120120000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:120108400-120120000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:120108400-120120200	Strong transcription	Osteobl	bone
28	chr12:120108600-120113200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:120108600-120116000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:120108600-120120200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:120108600-120120200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:120108800-120113000	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr12:120108800-120118000	Strong transcription	Liver	Liver
34	chr12:120108800-120118200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:120108800-120119400	Strong transcription	NHEK	skin
36	chr12:120108800-120119800	Strong transcription	Hela-S3	cervix
37	chr12:120108800-120120200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:120108800-120120200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:120108800-120120800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:120109000-120112200	Strong transcription	Brain Substantia Nigra	brain
41	chr12:120109000-120116200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:120109000-120119400	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr12:120109000-120120200	Strong transcription	Dnd41	blood
44	chr12:120109200-120112800	Strong transcription	HSMM	muscle
45	chr12:120109200-120113000	Genic enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:120109200-120120200	Strong transcription	Thymus	Thymus
47	chr12:120109200-120121200	Strong transcription	Fetal Stomach	stomach
48	chr12:120109400-120112800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
49	chr12:120109400-120113400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:120109400-120117000	Strong transcription	Fetal Brain Male	brain

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