Variant report

Variant	rs2158996
Chromosome Location	chr14:71529599-71529600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12100737	0.81[AMR][1000 genomes]
rs12101246	0.81[AMR][1000 genomes]
rs12896370	0.81[AMR][1000 genomes]
rs17093738	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17108808	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17108862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17108877	0.81[AMR][1000 genomes]
rs17108925	0.81[AMR][1000 genomes]
rs17109053	0.81[EUR][1000 genomes]
rs2158997	0.81[AMR][1000 genomes]
rs2240533	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286310	0.81[AMR][1000 genomes]
rs2526850	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2526851	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2526854	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2526857	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2526858	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2526872	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2526879	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2810075	0.83[AMR][1000 genomes]
rs2810096	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2810097	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2810099	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2810104	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2810105	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2810114	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs28374308	0.81[AMR][1000 genomes]
rs34257131	0.81[AMR][1000 genomes]
rs34368938	0.81[AMR][1000 genomes]
rs34488204	0.81[AMR][1000 genomes]
rs34763296	0.81[AMR][1000 genomes]
rs35631530	0.81[AMR][1000 genomes]
rs36555	0.82[AMR][1000 genomes]
rs36559	0.81[AMR][1000 genomes]
rs36567	0.81[AMR][1000 genomes]
rs3814869	0.81[AMR][1000 genomes]
rs3829954	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4048474	0.81[AMR][1000 genomes]
rs4132849	0.81[AMR][1000 genomes]
rs4426283	0.81[AMR][1000 genomes]
rs56021283	0.81[AMR][1000 genomes]
rs56043821	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56268907	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56306703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58133478	0.81[AMR][1000 genomes]
rs58984901	0.81[AMR][1000 genomes]
rs59699904	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61990379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61990380	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61990387	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61990419	0.80[AMR][1000 genomes]
rs61992065	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61992087	0.80[EUR][1000 genomes]
rs67188216	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7145484	0.81[AMR][1000 genomes]
rs7146932	0.81[AMR][1000 genomes]
rs7153237	0.81[AMR][1000 genomes]
rs7157250	0.81[AMR][1000 genomes]
rs8003227	0.80[AMR][1000 genomes]
rs8007026	0.81[AMR][1000 genomes]
rs8010063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8013146	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8014273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8016506	0.81[AMR][1000 genomes]
rs8181986	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

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
rs2158996	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2158996	PCNX	cis	Artery Aorta	GTEx
rs2158996	PCNX	cis	Thyroid	GTEx
rs2158996	PCNX	cis	Nerve Tibial	GTEx
rs2158996	PCNX	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71495800-71546200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71497000-71554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:71499600-71540800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:71507000-71531600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr14:71508000-71530800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:71510000-71531600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr14:71510000-71531800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr14:71510000-71532600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:71510200-71532000	Strong transcription	Primary B cells from peripheral blood	blood
10	chr14:71510200-71538200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr14:71510400-71530000	Strong transcription	Dnd41	blood
12	chr14:71510800-71531200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:71511000-71530600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:71511600-71540800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr14:71511600-71541000	Weak transcription	Pancreas	Pancrea
16	chr14:71512400-71531400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:71513400-71531200	Strong transcription	Primary B cells from cord blood	blood
18	chr14:71513400-71531600	Strong transcription	Fetal Intestine Large	intestine
19	chr14:71513800-71530200	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr14:71517400-71531600	Strong transcription	Primary T cells from cord blood	blood
21	chr14:71517800-71532400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr14:71518200-71531000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr14:71518200-71531200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:71518200-71544000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr14:71518400-71530200	Strong transcription	Adipose Nuclei	Adipose
26	chr14:71518400-71531200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr14:71518400-71531400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr14:71518400-71532400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr14:71518600-71531400	Strong transcription	HSMM	muscle
30	chr14:71520200-71531400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:71520400-71531400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:71521200-71529600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr14:71523200-71531000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr14:71524200-71529600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr14:71524200-71529800	Strong transcription	Ovary	ovary
36	chr14:71524200-71529800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr14:71524200-71530200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr14:71524200-71531200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr14:71524200-71531400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr14:71524200-71531600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr14:71524200-71531800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr14:71524200-71532600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr14:71524400-71529600	Strong transcription	Brain Germinal Matrix	brain
44	chr14:71524400-71530800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr14:71524400-71531800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr14:71525800-71539800	Weak transcription	Brain Substantia Nigra	brain
47	chr14:71526600-71529800	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr14:71526800-71531400	Weak transcription	Fetal Intestine Small	intestine
49	chr14:71527200-71536200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr14:71527400-71540000	Weak transcription	Brain Inferior Temporal Lobe	brain

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