Variant report

Variant	rs2286136
Chromosome Location	chr14:72168695-72168696
allele	C/T
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	FOXA1	chr14:72168638-72169045	HepG2	liver:	n/a	n/a
2	FOXA1	chr14:72168621-72169193	T-47D	breast:	n/a	n/a
3	POLR2A	chr14:72168231-72168695	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SIPA1L1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1005605	0.82[ASN][1000 genomes]
rs10132111	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10133626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10137642	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139519	1.00[JPT][hapmap]
rs1204988	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1204992	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1204995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1204996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1204997	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12880188	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12896900	1.00[JPT][hapmap]
rs1468373	0.82[ASN][1000 genomes]
rs1981588	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2286135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784064	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3825719	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4140797	0.82[ASN][1000 genomes]
rs4140799	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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]
rs7148679	0.82[ASN][1000 genomes]
rs7156313	1.00[JPT][hapmap]
rs7350725	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs757744	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8006300	0.82[CHD][hapmap]
rs8015004	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
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
rs2286136	PCNX	cis	cerebellum	SCAN
rs2286136	ACOT2	cis	parietal	SCAN

Chromatin state (count:116 , 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	chr14:72148200-72170000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:72148200-72175800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:72148200-72200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:72149000-72177800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr14:72149000-72186200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr14:72149800-72176000	Weak transcription	Small Intestine	intestine
12	chr14:72151400-72169600	Weak transcription	Fetal Brain Female	brain
13	chr14:72151600-72171800	Weak transcription	Left Ventricle	heart
14	chr14:72151600-72188000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:72151800-72171600	Weak transcription	Colonic Mucosa	Colon
16	chr14:72152400-72168800	Weak transcription	Esophagus	oesophagus
17	chr14:72152400-72171600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr14:72153000-72175800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr14:72153200-72175800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:72153600-72168800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr14:72154400-72169400	Weak transcription	Fetal Heart	heart
22	chr14:72156800-72176000	Weak transcription	HepG2	liver
23	chr14:72157000-72175800	Weak transcription	Fetal Intestine Large	intestine
24	chr14:72159600-72172000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr14:72159800-72170000	Weak transcription	Colon Smooth Muscle	Colon
26	chr14:72159800-72171600	Weak transcription	Pancreas	Pancrea
27	chr14:72159800-72172400	Weak transcription	Spleen	Spleen
28	chr14:72160200-72169200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr14:72160200-72169800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr14:72160200-72171400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr14:72160200-72171800	Weak transcription	Fetal Intestine Small	intestine
32	chr14:72160200-72176000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr14:72160200-72177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr14:72160200-72191400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr14:72160200-72202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr14:72160400-72169000	Weak transcription	NHLF	lung
37	chr14:72160800-72175400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr14:72161000-72169000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:72161000-72169800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:72161200-72169400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr14:72161200-72171800	Weak transcription	Thymus	Thymus
42	chr14:72162600-72169800	Weak transcription	Brain Substantia Nigra	brain
43	chr14:72162600-72176000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr14:72163800-72177800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr14:72164000-72169600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr14:72164000-72171600	Weak transcription	Gastric	stomach
47	chr14:72164200-72169600	Weak transcription	Brain Hippocampus Middle	brain
48	chr14:72164200-72178600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr14:72164600-72169000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr14:72164800-72172800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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