Variant report

Variant	rs2526884
Chromosome Location	chr14:71367967-71367968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71367722..71371068-chr14:71372863..71375706,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10132789	0.82[EUR][1000 genomes]
rs10132984	0.83[EUR][1000 genomes]
rs10140225	0.82[EUR][1000 genomes]
rs10140917	0.81[EUR][1000 genomes]
rs10145824	0.90[EUR][1000 genomes]
rs10148324	0.89[EUR][1000 genomes]
rs11623266	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12896829	0.87[EUR][1000 genomes]
rs1978164	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2010713	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097975	0.82[EUR][1000 genomes]
rs2240341	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251394	0.91[EUR][1000 genomes]
rs2332506	0.86[EUR][1000 genomes]
rs2526847	0.92[EUR][1000 genomes]
rs2526848	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526856	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526859	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526864	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526871	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526873	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526875	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526880	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526881	0.84[ASN][1000 genomes]
rs2526883	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526887	0.85[ASN][1000 genomes]
rs2810072	0.85[EUR][1000 genomes]
rs2810074	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2810077	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2810078	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2810079	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810081	0.88[ASN][1000 genomes]
rs2810082	0.89[ASN][1000 genomes]
rs2810101	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2810109	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2810111	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810113	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2810118	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2877708	0.82[EUR][1000 genomes]
rs3784067	0.81[EUR][1000 genomes]
rs4132848	0.89[EUR][1000 genomes]
rs4147077	0.89[EUR][1000 genomes]
rs4366661	0.89[EUR][1000 genomes]
rs4467005	0.81[EUR][1000 genomes]
rs4531677	0.83[EUR][1000 genomes]
rs58938327	0.87[EUR][1000 genomes]
rs714421	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7144986	0.86[EUR][1000 genomes]
rs7147862	0.89[EUR][1000 genomes]
rs7150037	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7151145	0.81[ASN][1000 genomes]
rs7154437	0.91[EUR][1000 genomes]
rs7160958	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8004452	0.84[EUR][1000 genomes]
rs8006046	0.81[EUR][1000 genomes]
rs8007425	0.80[EUR][1000 genomes]
rs917067	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9323556	0.86[EUR][1000 genomes]
rs9323557	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv1039769	chr14:71310954-71525720	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv542128	chr14:71310954-71525720	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1053303	chr14:71316325-71402971	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2526884	PCNX	cis	Esophagus Muscularis	GTEx
rs2526884	PCNX	cis	Thyroid	GTEx
rs2526884	PCNX	cis	Artery Aorta	GTEx
rs2526884	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2526884	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs2526884	PCNX	cis	Artery Tibial	GTEx
rs2526884	PCNX	cis	Nerve Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71350600-71373000	Weak transcription	Spleen	Spleen
2	chr14:71355000-71371600	Weak transcription	Placenta	Placenta
3	chr14:71361800-71373400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr14:71362200-71368200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:71362200-71370800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr14:71362200-71371600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:71362400-71371600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:71363800-71368800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr14:71364000-71373800	Weak transcription	Small Intestine	intestine
10	chr14:71364200-71368200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:71364200-71368200	Weak transcription	Aorta	Aorta
12	chr14:71364200-71373000	Weak transcription	NHEK	skin
13	chr14:71364200-71373600	Weak transcription	Lung	lung
14	chr14:71365200-71368800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr14:71365400-71368200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:71365400-71368200	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:71365400-71368600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr14:71365400-71370800	Weak transcription	Fetal Lung	lung
19	chr14:71365400-71371000	Weak transcription	HSMMtube	muscle
20	chr14:71365400-71371600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr14:71365400-71373400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr14:71365600-71370600	Weak transcription	Fetal Stomach	stomach
23	chr14:71365600-71371000	Weak transcription	Ovary	ovary
24	chr14:71365600-71371200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr14:71365600-71371600	Weak transcription	Right Atrium	heart
26	chr14:71366000-71368000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr14:71366000-71368200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:71366000-71368200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr14:71366000-71368200	Weak transcription	NHDF-Ad	bronchial
30	chr14:71366200-71371600	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:71367600-71368200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:71367600-71368200	Enhancers	NH-A	brain
33	chr14:71367600-71368600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr14:71367600-71369000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr14:71367600-71369200	Enhancers	Osteobl	bone
36	chr14:71367600-71370400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr14:71367800-71368200	Enhancers	Primary hematopoietic stem cells	blood
38	chr14:71367800-71368200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr14:71367800-71368600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr14:71367800-71368600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr14:71367800-71368600	Enhancers	HSMM	muscle
42	chr14:71367800-71368800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr14:71367800-71368800	Enhancers	NHLF	lung
44	chr14:71367800-71369200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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