Variant report

Variant	rs1012725
Chromosome Location	chr14:71605711-71605712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:71605350..71606109-chr14:71870362..71870894,2	MCF-7	breast:
2	chr14:71605592..71606386-chr14:71869586..71870379,2	MCF-7	breast:
3	chr14:71605403..71606379-chr14:72219242..72220271,11	MCF-7	breast:
4	chr14:71605416..71606618-chr14:72219460..72220340,5	MCF-7	breast:
5	chr14:71604707..71606600-chr14:72213499..72215384,2	MCF-7	breast:
6	chr14:71604769..71607668-chr14:71786929..71789620,2	MCF-7	breast:
7	chr14:71605408..71606120-chr14:72322432..72323318,2	K562	blood:
8	chr14:71605537..71606405-chr14:72219506..72220423,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17093738	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17109053	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240533	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs2526850	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs2526857	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs2526858	0.81[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[YRI][hapmap]
rs2810097	0.81[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap]
rs2810099	0.81[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2810104	0.80[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap]
rs56022326	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56043821	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56268907	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58815178	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59699904	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61992065	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61992087	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8010063	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs8014273	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs8181986	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	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
7	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
8	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
9	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats 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
10	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1012725	PCNX	cis	Artery Tibial	GTEx
rs1012725	PCNX	cis	Artery Aorta	GTEx
rs1012725	PCNX	cis	Nerve Tibial	GTEx
rs1012725	PCNX	cis	Thyroid	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71598400-71608600	Weak transcription	NHLF	lung
2	chr14:71604400-71606400	Enhancers	NH-A	brain
3	chr14:71604600-71608400	Weak transcription	Spleen	Spleen
4	chr14:71605000-71605800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:71605000-71605800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr14:71605200-71605800	Enhancers	Fetal Brain Female	brain
7	chr14:71605200-71605800	Enhancers	HMEC	breast
8	chr14:71605200-71606200	Enhancers	NHEK	skin
9	chr14:71605200-71606400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr14:71605200-71606400	Enhancers	Hela-S3	cervix
11	chr14:71605400-71605800	Enhancers	Brain Cingulate Gyrus	brain
12	chr14:71605400-71605800	Enhancers	Brain Hippocampus Middle	brain
13	chr14:71605400-71606000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr14:71605400-71606000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr14:71605400-71606000	Enhancers	Fetal Heart	heart
16	chr14:71605400-71606200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr14:71605400-71606200	Enhancers	Brain Substantia Nigra	brain
18	chr14:71605400-71606200	Enhancers	Fetal Brain Male	brain
19	chr14:71605400-71606600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr14:71605600-71605800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr14:71605600-71605800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:71605600-71605800	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr14:71605600-71605800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr14:71605600-71605800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr14:71605600-71605800	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr14:71605600-71605800	Enhancers	Right Ventricle	heart
27	chr14:71605600-71605800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr14:71605600-71605800	Enhancers	HUVEC	blood vessel
29	chr14:71605600-71605800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr14:71605600-71606000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:71605600-71606000	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr14:71605600-71606000	Enhancers	Colon Smooth Muscle	Colon
33	chr14:71605600-71606000	Enhancers	Fetal Muscle Leg	muscle
34	chr14:71605600-71606000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr14:71605600-71606000	Enhancers	Stomach Mucosa	stomach
36	chr14:71605600-71606200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr14:71605600-71606200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr14:71605600-71606200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr14:71605600-71606200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:71605600-71606200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr14:71605600-71606200	Enhancers	Primary B cells from peripheral blood	blood
42	chr14:71605600-71606200	Enhancers	Primary T cells from cord blood	blood
43	chr14:71605600-71606200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr14:71605600-71606200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr14:71605600-71606200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr14:71605600-71606200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr14:71605600-71606200	Enhancers	Duodenum Mucosa	Duodenum
48	chr14:71605600-71606200	Enhancers	Esophagus	oesophagus
49	chr14:71605600-71606200	Enhancers	Fetal Kidney	kidney
50	chr14:71605600-71606200	Enhancers	Fetal Stomach	stomach

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