Variant report

Variant	rs8015004
Chromosome Location	chr14:72173413-72173414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1005605	0.85[ASN][1000 genomes]
rs10132111	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10133626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10137642	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10139519	1.00[JPT][hapmap]
rs1204988	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1204992	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1204995	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1204996	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1204997	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12880188	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs1468373	0.85[ASN][1000 genomes]
rs1981588	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2286135	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286136	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784064	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3825719	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4140799	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899398	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7140501	1.00[JPT][hapmap]
rs7142343	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7156313	1.00[JPT][hapmap]
rs7350725	0.96[CEU][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs757744	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8006300	0.82[CHD][hapmap]
rs9672060	0.93[CHD][hapmap];1.00[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	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1047559	chr14:72151736-72282151	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8015004	PCNX	cis	cerebellum	SCAN
rs8015004	ACOT2	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72118600-72191400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr14:72129400-72196800	Weak transcription	Right Ventricle	heart
3	chr14:72140600-72176000	Weak transcription	Hela-S3	cervix
4	chr14:72142000-72191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr14:72147800-72185000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr14:72148200-72175800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr14:72148200-72200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr14:72149000-72177800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr14:72149000-72186200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr14:72149800-72176000	Weak transcription	Small Intestine	intestine
11	chr14:72151600-72188000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:72153000-72175800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr14:72153200-72175800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:72156800-72176000	Weak transcription	HepG2	liver
15	chr14:72157000-72175800	Weak transcription	Fetal Intestine Large	intestine
16	chr14:72160200-72176000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr14:72160200-72177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr14:72160200-72191400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr14:72160200-72202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr14:72160800-72175400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr14:72162600-72176000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:72163800-72177800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr14:72164200-72178600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr14:72165200-72202000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr14:72165400-72180600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr14:72165800-72178600	Weak transcription	Ovary	ovary
27	chr14:72166400-72176000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:72166400-72176000	Weak transcription	Adipose Nuclei	Adipose
29	chr14:72166800-72196400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr14:72167200-72176000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr14:72167400-72191000	Weak transcription	Fetal Thymus	thymus
32	chr14:72168000-72191800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr14:72168600-72174400	Strong transcription	Liver	Liver
34	chr14:72168800-72181600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr14:72168800-72185000	Strong transcription	Primary B cells from cord blood	blood
36	chr14:72168800-72201600	Weak transcription	Stomach Mucosa	stomach
37	chr14:72169200-72191400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:72169400-72178400	Weak transcription	HUVEC	blood vessel
39	chr14:72169800-72173800	Strong transcription	Primary T cells from cord blood	blood
40	chr14:72169800-72175800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:72169800-72175800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr14:72170200-72173600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr14:72170400-72176000	Weak transcription	Brain Substantia Nigra	brain
44	chr14:72170400-72177800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr14:72170400-72178400	Weak transcription	Colon Smooth Muscle	Colon
46	chr14:72170600-72173800	Strong transcription	HSMM	muscle
47	chr14:72170600-72173800	Weak transcription	HSMMtube	muscle
48	chr14:72170600-72175200	Weak transcription	Placenta	Placenta
49	chr14:72170600-72175800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr14:72170600-72175800	Weak transcription	NHLF	lung

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