Variant report

Variant	rs2810116
Chromosome Location	chr14:71391933-71391934
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71378921..71381459-chr14:71390825..71392481,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1018977	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12100737	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12101246	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12883437	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12892739	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12896370	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17108804	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17108822	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17108877	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17108925	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17108967	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1859468	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2010061	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2097866	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2158997	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2189806	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2189807	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2286310	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2332477	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526846	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526852	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526855	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526860	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526862	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526874	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526876	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526877	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526878	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526882	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526886	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526890	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810071	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810073	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810098	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810100	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810107	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810115	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810117	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28374308	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34049963	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34257131	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34368938	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34488204	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34731365	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34763296	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35631530	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814869	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3814871	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4048474	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4132849	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4391999	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4426283	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56021283	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58133478	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58984901	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61990419	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7145484	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7146591	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7146932	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7153237	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7157250	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003103	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8003227	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8007026	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8012728	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8016506	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8022768	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917065	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs989501	0.88[AMR][1000 genomes];0.86[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2810116	PCNX	cis	Artery Aorta	GTEx
rs2810116	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs2810116	PCNX	cis	Nerve Tibial	GTEx
rs2810116	PCNX	cis	Artery Tibial	GTEx
rs2810116	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2810116	PCNX	cis	Thyroid	GTEx

Chromatin state (count:83 , 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	chr14:71376600-71398400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr14:71377400-71395000	Weak transcription	Brain Angular Gyrus	brain
6	chr14:71377400-71396800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr14:71378000-71393000	Weak transcription	Right Atrium	heart
8	chr14:71378000-71400600	Weak transcription	Fetal Kidney	kidney
9	chr14:71379600-71392800	Weak transcription	Ovary	ovary
10	chr14:71379600-71408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr14:71379600-71410400	Weak transcription	Aorta	Aorta
12	chr14:71380000-71398200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr14:71380400-71400800	Weak transcription	Fetal Intestine Large	intestine
14	chr14:71380600-71394200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr14:71381000-71392600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr14:71381400-71394000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr14:71381600-71394400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr14:71382400-71394200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr14:71384000-71392200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:71384000-71401200	Weak transcription	Fetal Muscle Leg	muscle
21	chr14:71384200-71393000	Weak transcription	Fetal Brain Female	brain
22	chr14:71384200-71395000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:71384200-71408400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr14:71384600-71402000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr14:71386800-71392600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr14:71386800-71393000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:71386800-71393000	Weak transcription	Left Ventricle	heart
28	chr14:71386800-71393000	Weak transcription	Right Ventricle	heart
29	chr14:71386800-71396800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr14:71386800-71400600	Weak transcription	Fetal Stomach	stomach
31	chr14:71387000-71392800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr14:71387000-71396600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr14:71387000-71398000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr14:71387200-71393000	Weak transcription	Primary B cells from cord blood	blood
35	chr14:71387200-71408400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:71387600-71392600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr14:71387600-71392600	Weak transcription	Colon Smooth Muscle	Colon
38	chr14:71387600-71392600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr14:71387600-71392800	Weak transcription	Brain Substantia Nigra	brain
40	chr14:71387600-71393000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:71387800-71393000	Weak transcription	Psoas Muscle	Psoas
42	chr14:71388000-71392400	Weak transcription	Liver	Liver
43	chr14:71388200-71392400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr14:71388200-71392800	Weak transcription	Adipose Nuclei	Adipose
45	chr14:71388200-71392800	Weak transcription	Fetal Lung	lung
46	chr14:71388200-71402000	Weak transcription	HSMM	muscle
47	chr14:71388200-71410400	Weak transcription	Thymus	Thymus
48	chr14:71388400-71400800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr14:71388800-71392600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:71388800-71393000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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