Variant report

Variant	rs2526872
Chromosome Location	chr14:71384885-71384886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71373112..71375503-chr14:71384629..71386969,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17108808	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108862	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2158996	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2189806	0.81[AMR][1000 genomes]
rs2526850	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526851	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526854	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526857	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526858	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526874	0.81[AMR][1000 genomes]
rs2526879	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810073	0.81[AMR][1000 genomes]
rs2810075	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2810096	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810097	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810099	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2810104	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2810105	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2810114	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810117	0.81[AMR][1000 genomes]
rs36555	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36559	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36567	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3829954	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56306703	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61990379	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61990380	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61990387	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8010063	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8013146	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8014273	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2526872	PCNX	cis	Artery Tibial	GTEx
rs2526872	PCNX	cis	Artery Aorta	GTEx
rs2526872	PCNX	cis	Nerve Tibial	GTEx
rs2526872	PCNX	cis	Thyroid	GTEx
rs2526872	PCNX	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71375600-71398400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:71376000-71396800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr14:71376000-71401000	Weak transcription	Lung	lung
4	chr14:71376600-71385400	Weak transcription	HUVEC	blood vessel
5	chr14:71376600-71386000	Weak transcription	Fetal Lung	lung
6	chr14:71376600-71389000	Weak transcription	HSMMtube	muscle
7	chr14:71376600-71398400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:71376800-71386200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr14:71377200-71386600	Weak transcription	NHDF-Ad	bronchial
10	chr14:71377400-71385200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr14:71377400-71385400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:71377400-71385600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:71377400-71387400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:71377400-71391400	Weak transcription	Esophagus	oesophagus
15	chr14:71377400-71395000	Weak transcription	Brain Angular Gyrus	brain
16	chr14:71377400-71396800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr14:71377600-71386200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr14:71377800-71386000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:71377800-71386600	Weak transcription	Colon Smooth Muscle	Colon
20	chr14:71377800-71386600	Weak transcription	NHLF	lung
21	chr14:71378000-71385600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr14:71378000-71385600	Weak transcription	NH-A	brain
23	chr14:71378000-71386000	Weak transcription	A549	lung
24	chr14:71378000-71386200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:71378000-71386400	Weak transcription	Fetal Brain Male	brain
26	chr14:71378000-71386600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr14:71378000-71393000	Weak transcription	Right Atrium	heart
28	chr14:71378000-71400600	Weak transcription	Fetal Kidney	kidney
29	chr14:71378400-71385800	Weak transcription	NHEK	skin
30	chr14:71378400-71386600	Weak transcription	HMEC	breast
31	chr14:71378600-71385200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:71378600-71386600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr14:71379400-71385400	Weak transcription	Brain Hippocampus Middle	brain
34	chr14:71379600-71386600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr14:71379600-71392800	Weak transcription	Ovary	ovary
36	chr14:71379600-71408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:71379600-71410400	Weak transcription	Aorta	Aorta
38	chr14:71379800-71385200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr14:71379800-71385600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr14:71379800-71385800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr14:71379800-71386600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr14:71379800-71386600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr14:71380000-71385400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:71380000-71385600	Weak transcription	Left Ventricle	heart
45	chr14:71380000-71386600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr14:71380000-71387200	Weak transcription	Hela-S3	cervix
47	chr14:71380000-71398200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr14:71380400-71400800	Weak transcription	Fetal Intestine Large	intestine
49	chr14:71380600-71394200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr14:71381000-71392600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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