Variant report

Variant	rs2526852
Chromosome Location	chr14:71416167-71416168
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	chr14:71372532..71376222-chr14:71415679..71419226,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1018977	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12100737	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12101246	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12883437	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12892739	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12896370	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12897533	0.81[AMR][1000 genomes]
rs17108804	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17108822	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17108877	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17108925	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17108967	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1859468	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2010061	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2097866	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2158997	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2189806	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs221909	0.81[AMR][1000 genomes]
rs221912	0.80[AMR][1000 genomes]
rs221920	0.80[AMR][1000 genomes]
rs221921	0.81[AMR][1000 genomes]
rs221922	0.81[AMR][1000 genomes]
rs221923	0.81[AMR][1000 genomes]
rs221927	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2286310	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2332477	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526846	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2526855	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526860	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526862	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526874	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526876	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526877	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526878	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526882	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526886	0.84[AMR][1000 genomes]
rs2526890	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810071	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810073	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810098	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810100	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810107	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2810115	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810116	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810117	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28374308	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34049963	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34257131	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34368938	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34488204	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34731365	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34763296	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35631530	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3814869	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3814871	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4048474	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4132849	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4391999	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4426283	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56021283	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58133478	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58984901	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61990419	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67981189	0.87[AMR][1000 genomes]
rs7145484	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7146591	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7146932	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7153237	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7157250	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8003103	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003227	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8007026	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8012728	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8016506	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8022768	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs917065	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs989501	0.80[AMR][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	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
12	esv3434532	chr14:71414399-71417147	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2526852	PCNX	cis	Artery Aorta	GTEx
rs2526852	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2526852	PCNX	cis	Thyroid	GTEx
rs2526852	PCNX	cis	Nerve Tibial	GTEx
rs2526852	PCNX	cis	Artery Tibial	GTEx
rs2526852	PCNX	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:118 , 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	chr14:71402200-71442800	Weak transcription	HSMMtube	muscle
3	chr14:71408400-71416800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr14:71408600-71417000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:71409200-71416600	ZNF genes & repeats	GM12878-XiMat	blood
6	chr14:71409200-71417200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr14:71411000-71416200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:71411000-71416400	Weak transcription	Colonic Mucosa	Colon
9	chr14:71411000-71443200	Weak transcription	Hela-S3	cervix
10	chr14:71411000-71443600	Weak transcription	NHLF	lung
11	chr14:71411000-71443800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:71411000-71443800	Weak transcription	Gastric	stomach
13	chr14:71411200-71428400	Weak transcription	NH-A	brain
14	chr14:71411400-71419400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr14:71411400-71429200	Weak transcription	HUVEC	blood vessel
16	chr14:71411400-71444000	Weak transcription	Brain Angular Gyrus	brain
17	chr14:71411800-71444200	Weak transcription	Fetal Brain Male	brain
18	chr14:71412400-71419600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr14:71412800-71416800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr14:71412800-71420000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:71413000-71418000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:71413400-71416600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr14:71413600-71416600	Strong transcription	Osteobl	bone
24	chr14:71413600-71416800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:71413600-71416800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:71413600-71418800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr14:71413800-71416600	Strong transcription	Brain Anterior Caudate	brain
28	chr14:71413800-71417000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:71414000-71416200	Weak transcription	HSMM	muscle
30	chr14:71414000-71433000	Weak transcription	NHEK	skin
31	chr14:71414400-71417000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:71414400-71418400	Strong transcription	A549	lung
33	chr14:71414400-71443400	Weak transcription	Fetal Kidney	kidney
34	chr14:71414600-71418800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr14:71414600-71419600	Weak transcription	Psoas Muscle	Psoas
36	chr14:71414800-71416600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr14:71414800-71416800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr14:71414800-71417000	Strong transcription	Liver	Liver
39	chr14:71414800-71417800	Weak transcription	HepG2	liver
40	chr14:71414800-71419200	Weak transcription	Fetal Heart	heart
41	chr14:71414800-71420800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr14:71414800-71422200	Weak transcription	Colon Smooth Muscle	Colon
43	chr14:71414800-71422800	Weak transcription	Brain Substantia Nigra	brain
44	chr14:71414800-71428400	Weak transcription	HMEC	breast
45	chr14:71414800-71428800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr14:71414800-71436800	Weak transcription	Fetal Brain Female	brain
47	chr14:71414800-71438800	Weak transcription	Small Intestine	intestine
48	chr14:71414800-71443600	Weak transcription	Brain Hippocampus Middle	brain
49	chr14:71414800-71443600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr14:71414800-71443800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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