Variant report

Variant	rs2270040
Chromosome Location	chr14:71556455-71556456
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17108824	0.88[AFR][1000 genomes]
rs17108910	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1859915	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2526866	0.82[AFR][1000 genomes]
rs45483794	0.90[EUR][1000 genomes]
rs55685004	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2270040	PCNX	cis	Artery Tibial	GTEx
rs2270040	PCNX	Cis_1M	lymphoblastoid	RTeQTL

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	chr14:71544400-71568800	Weak transcription	Gastric	stomach
3	chr14:71544800-71561400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:71544800-71571800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:71544800-71572000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr14:71544800-71575400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:71544800-71581400	Weak transcription	Small Intestine	intestine
8	chr14:71545400-71557600	Weak transcription	Brain Angular Gyrus	brain
9	chr14:71545400-71559400	Weak transcription	NHEK	skin
10	chr14:71545400-71570000	Weak transcription	Psoas Muscle	Psoas
11	chr14:71545400-71572000	Weak transcription	Hela-S3	cervix
12	chr14:71545400-71574800	Weak transcription	NHLF	lung
13	chr14:71545800-71558400	Weak transcription	Colonic Mucosa	Colon
14	chr14:71545800-71558800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr14:71545800-71563600	Weak transcription	Fetal Brain Male	brain
16	chr14:71549200-71561800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr14:71549800-71562800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:71550200-71557400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:71550600-71556800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr14:71550600-71561600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr14:71550600-71562800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr14:71550800-71557600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:71550800-71562600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr14:71551200-71558200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
25	chr14:71551400-71556600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr14:71551400-71562000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr14:71551600-71556600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:71551600-71558600	Strong transcription	Primary hematopoietic stem cells	blood
29	chr14:71551600-71560200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr14:71551600-71561800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr14:71551600-71562000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:71551600-71562800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:71551800-71557800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
34	chr14:71551800-71559400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr14:71551800-71561200	Strong transcription	Primary B cells from cord blood	blood
36	chr14:71551800-71561400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:71551800-71561600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr14:71551800-71561600	Strong transcription	Fetal Intestine Large	intestine
39	chr14:71552000-71563600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr14:71552000-71588400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr14:71552400-71557600	Weak transcription	Thymus	Thymus
42	chr14:71552400-71559000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr14:71552400-71559400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr14:71552400-71571200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:71552600-71558800	Weak transcription	Fetal Brain Female	brain
46	chr14:71552600-71568800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr14:71553600-71557600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:71553600-71558600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr14:71553600-71558600	Weak transcription	Fetal Stomach	stomach
50	chr14:71553600-71558800	Weak transcription	Fetal Intestine Small	intestine

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