Variant report

Variant	rs757744
Chromosome Location	chr14:72197773-72197774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1005605	0.94[ASN][1000 genomes]
rs10132111	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10133626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10137642	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10139519	1.00[JPT][hapmap]
rs1204988	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1204992	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204995	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1204996	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1204997	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12880188	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1468373	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981588	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2286135	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286136	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3784064	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3825719	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4140799	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4899398	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7140501	1.00[JPT][hapmap]
rs7142343	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7156313	1.00[JPT][hapmap]
rs7350725	0.92[CEU][hapmap];0.81[CHD][hapmap]
rs8015004	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9672060	0.86[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs757744	PCNX	cis	parietal	SCAN
rs757744	ACOT2	cis	parietal	SCAN
rs757744	PCNX	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72148200-72200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:72160200-72202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr14:72165200-72202000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:72168800-72201600	Weak transcription	Stomach Mucosa	stomach
5	chr14:72176400-72200000	Weak transcription	Small Intestine	intestine
6	chr14:72182200-72207400	Strong transcription	GM12878-XiMat	blood
7	chr14:72185800-72206200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr14:72187000-72204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr14:72187600-72206200	Strong transcription	Dnd41	blood
10	chr14:72187600-72207600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr14:72187800-72206200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr14:72188200-72206400	Strong transcription	Primary T cells from cord blood	blood
13	chr14:72188600-72206000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr14:72188800-72199400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:72188800-72205800	Strong transcription	Fetal Intestine Large	intestine
16	chr14:72188800-72207600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr14:72189600-72204400	Strong transcription	Fetal Stomach	stomach
18	chr14:72189800-72205800	Strong transcription	Fetal Intestine Small	intestine
19	chr14:72189800-72206000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr14:72189800-72206000	Strong transcription	Spleen	Spleen
21	chr14:72189800-72206600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:72189800-72206800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr14:72189800-72206800	Strong transcription	Primary B cells from cord blood	blood
24	chr14:72190000-72206000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr14:72190000-72206000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr14:72190200-72206000	Strong transcription	Placenta	Placenta
27	chr14:72190600-72214200	Weak transcription	K562	blood
28	chr14:72191400-72206000	Strong transcription	Liver	Liver
29	chr14:72191600-72197800	Genic enhancers	Osteobl	bone
30	chr14:72191600-72206000	Strong transcription	Gastric	stomach
31	chr14:72191600-72206000	Strong transcription	Pancreas	Pancrea
32	chr14:72192200-72197800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr14:72192400-72202000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr14:72192800-72198400	Weak transcription	Hela-S3	cervix
35	chr14:72193000-72207200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr14:72193400-72204000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr14:72193600-72198200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr14:72193800-72204400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:72194000-72197800	Weak transcription	Fetal Heart	heart
40	chr14:72194000-72199400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:72194000-72199400	Weak transcription	NHDF-Ad	bronchial
42	chr14:72194000-72199800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr14:72194200-72199000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr14:72194200-72204200	Weak transcription	Fetal Brain Male	brain
45	chr14:72194200-72204400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr14:72194600-72214800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr14:72194800-72203600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr14:72195000-72205400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr14:72195000-72206400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr14:72195200-72205600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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