Variant report

Variant	rs4899382
Chromosome Location	chr14:71574991-71574992
allele	A/G
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	STAT3	chr14:71574910-71575106	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PCNX	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10140225	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10140917	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10150408	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs116016	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs1468470	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1558097	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs221889	1.00[JPT][hapmap]
rs221892	1.00[JPT][hapmap]
rs221893	1.00[JPT][hapmap]
rs221897	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs221898	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs221924	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2240531	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2251394	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2286311	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2526847	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2526856	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2526859	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2526867	0.81[CHB][hapmap]
rs2526875	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2810113	0.81[CHB][hapmap]
rs2877714	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3784067	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4132848	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4366661	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4467005	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4531677	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6573994	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7143595	0.90[CHB][hapmap]
rs7144986	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7145285	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7152845	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7154395	0.82[ASN][1000 genomes]
rs7154437	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7155247	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156009	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs7158260	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8005160	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs8006046	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs8007425	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs8008111	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs8020480	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs8021824	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9323556	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9323557	0.90[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv565043	chr14:71395604-71625112	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4899382	PAPLN	cis	cerebellum	SCAN
rs4899382	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs4899382	PCNX	cis	parietal	SCAN
rs4899382	PCNX	cis	Artery Tibial	GTEx
rs4899382	COX16	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71538800-71584800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:71544800-71575400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:71544800-71581400	Weak transcription	Small Intestine	intestine
4	chr14:71552000-71588400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:71553600-71575200	Weak transcription	Aorta	Aorta
6	chr14:71553600-71575200	Weak transcription	Right Ventricle	heart
7	chr14:71553600-71575400	Weak transcription	Spleen	Spleen
8	chr14:71556000-71575400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr14:71556000-71582200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr14:71556400-71576000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr14:71556400-71583000	Weak transcription	Brain Substantia Nigra	brain
12	chr14:71557200-71576000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr14:71557200-71582000	Weak transcription	HUVEC	blood vessel
14	chr14:71557400-71575400	Weak transcription	Colon Smooth Muscle	Colon
15	chr14:71557800-71575200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr14:71558800-71576400	Weak transcription	Fetal Kidney	kidney
17	chr14:71558800-71576600	Weak transcription	Colonic Mucosa	Colon
18	chr14:71559600-71575400	Weak transcription	Brain Germinal Matrix	brain
19	chr14:71559800-71575200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr14:71559800-71575400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:71559800-71584000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr14:71564000-71575400	Weak transcription	Fetal Brain Female	brain
23	chr14:71564000-71583600	Weak transcription	Fetal Brain Male	brain
24	chr14:71566600-71582200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr14:71566600-71582600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr14:71566800-71582400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr14:71566800-71583400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr14:71566800-71585800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr14:71567200-71578800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr14:71567200-71581600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr14:71567200-71583800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr14:71567400-71581600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr14:71567600-71577800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:71567600-71578800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr14:71567600-71582600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr14:71568000-71577800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr14:71568200-71576400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr14:71568400-71578800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr14:71568600-71577800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr14:71568600-71578400	Strong transcription	Liver	Liver
41	chr14:71568600-71578600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr14:71568600-71578800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr14:71568800-71576600	Strong transcription	Fetal Stomach	stomach
44	chr14:71568800-71577600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr14:71568800-71577600	Strong transcription	Fetal Intestine Large	intestine
46	chr14:71568800-71577600	Strong transcription	GM12878-XiMat	blood
47	chr14:71568800-71577800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr14:71568800-71578200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr14:71568800-71578200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr14:71568800-71578800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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