Variant report

Variant	rs2526857
Chromosome Location	chr14:71412626-71412627
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	chr14:71373548..71375387-chr14:71412068..71413840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1012725	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs17108808	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108862	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17109053	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2158996	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2240533	0.95[CHB][hapmap];0.80[AMR][1000 genomes]
rs2526850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526851	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526853	0.86[AMR][1000 genomes]
rs2526854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526855	0.81[AMR][1000 genomes]
rs2526858	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526860	0.81[AMR][1000 genomes]
rs2526862	0.81[AMR][1000 genomes]
rs2526868	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2526872	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526879	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810075	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2810096	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810097	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2810099	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810105	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810114	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36555	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36559	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36567	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3829954	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56043821	0.83[AMR][1000 genomes]
rs56306703	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61990379	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61990380	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61990387	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67188216	0.80[AFR][1000 genomes]
rs7145558	0.84[AMR][1000 genomes]
rs8010063	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8013146	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8014273	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2526857	PCNX	cis	Artery Tibial	GTEx
rs2526857	PCNX	cis	Artery Aorta	GTEx
rs2526857	PCNX	cis	Thyroid	GTEx
rs2526857	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2526857	PCNX	cis	Nerve Tibial	GTEx
rs2526857	PCNX	cis	normal skin	skin_eQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71401000-71443800	Weak transcription	Right Ventricle	heart
2	chr14:71402200-71413600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr14:71402200-71413600	Weak transcription	Osteobl	bone
4	chr14:71402200-71442800	Weak transcription	HSMMtube	muscle
5	chr14:71402400-71413600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:71402400-71413600	Weak transcription	Fetal Kidney	kidney
7	chr14:71402400-71414400	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:71402600-71413800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr14:71406000-71413800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr14:71407200-71413600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr14:71408200-71412800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:71408400-71412800	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr14:71408400-71415200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr14:71408400-71416800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr14:71408600-71414800	ZNF genes & repeats	Dnd41	blood
16	chr14:71408600-71415000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr14:71408600-71417000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr14:71409000-71413000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr14:71409000-71415000	ZNF genes & repeats	Primary B cells from cord blood	blood
20	chr14:71409200-71415000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
21	chr14:71409200-71415200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr14:71409200-71416600	ZNF genes & repeats	GM12878-XiMat	blood
23	chr14:71409200-71417200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr14:71410400-71412800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:71410400-71415200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr14:71410800-71414200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:71410800-71414600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:71411000-71413400	Weak transcription	Fetal Lung	lung
29	chr14:71411000-71413400	Weak transcription	NHDF-Ad	bronchial
30	chr14:71411000-71413400	Weak transcription	NHEK	skin
31	chr14:71411000-71413600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr14:71411000-71413600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:71411000-71413600	Weak transcription	Adipose Nuclei	Adipose
34	chr14:71411000-71413600	Weak transcription	Liver	Liver
35	chr14:71411000-71413800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:71411000-71414000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:71411000-71414000	Weak transcription	Left Ventricle	heart
38	chr14:71411000-71414000	Weak transcription	Ovary	ovary
39	chr14:71411000-71414200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr14:71411000-71414200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr14:71411000-71414400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr14:71411000-71414400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr14:71411000-71414400	Weak transcription	Aorta	Aorta
44	chr14:71411000-71414400	Weak transcription	Brain Hippocampus Middle	brain
45	chr14:71411000-71414400	Weak transcription	Esophagus	oesophagus
46	chr14:71411000-71414600	Weak transcription	Pancreas	Pancrea
47	chr14:71411000-71415800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr14:71411000-71416200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr14:71411000-71416400	Weak transcription	Colonic Mucosa	Colon
50	chr14:71411000-71443200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links