Variant report

Variant	rs17109053
Chromosome Location	chr14:71609698-71609699
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71608562..71610263-chr14:71786915..71789760,2	MCF-7	breast:
2	chr14:71609565..71610435-chr14:73603108..73603774,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP3K9-10	chr14:71607842-71609970	ENSG00000269927.1

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000080815	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1012725	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]
rs17093738	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2158996	0.81[EUR][1000 genomes]
rs2240533	0.87[CHB][hapmap]
rs2526850	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2526857	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2526858	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2810097	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2810099	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2810104	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs56022326	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56043821	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56268907	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56306703	0.82[EUR][1000 genomes]
rs58815178	0.82[ASN][1000 genomes]
rs59699904	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61992065	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61992087	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8010063	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs8014273	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs8181986	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[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
rs17109053	PCNX	cis	Artery Tibial	GTEx
rs17109053	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs17109053	PCNX	cis	Thyroid	GTEx
rs17109053	PCNX	cis	Nerve Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71605600-71613200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr14:71605600-71613400	Enhancers	Placenta	Placenta
3	chr14:71606000-71610000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:71606000-71610000	Weak transcription	Stomach Mucosa	stomach
5	chr14:71606200-71610000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr14:71606200-71610000	Weak transcription	Brain Anterior Caudate	brain
7	chr14:71606200-71610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr14:71606200-71610800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:71606400-71609800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr14:71606400-71610000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr14:71606400-71610200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:71606400-71610200	Weak transcription	Adipose Nuclei	Adipose
13	chr14:71606400-71610200	Weak transcription	Liver	Liver
14	chr14:71606600-71610200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:71606600-71610200	Weak transcription	HSMMtube	muscle
16	chr14:71606600-71614800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:71607200-71610800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr14:71607400-71610000	Weak transcription	Fetal Intestine Large	intestine
19	chr14:71607600-71610800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr14:71607800-71610800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr14:71607800-71610800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr14:71607800-71610800	Enhancers	NHDF-Ad	bronchial
23	chr14:71608000-71611200	Enhancers	Primary B cells from cord blood	blood
24	chr14:71608200-71610200	Enhancers	Primary B cells from peripheral blood	blood
25	chr14:71608200-71610800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:71608200-71610800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr14:71608200-71610800	Enhancers	Osteobl	bone
28	chr14:71608400-71610400	Enhancers	Primary hematopoietic stem cells	blood
29	chr14:71608400-71610600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr14:71608400-71610600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr14:71608400-71610800	Enhancers	Primary T cells from cord blood	blood
32	chr14:71608400-71610800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr14:71608400-71610800	Enhancers	HepG2	liver
34	chr14:71608400-71610800	Enhancers	HMEC	breast
35	chr14:71608400-71610800	Enhancers	HSMM	muscle
36	chr14:71608400-71611000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr14:71608600-71610200	Enhancers	Fetal Thymus	thymus
38	chr14:71608600-71610400	Flanking Active TSS	NHEK	skin
39	chr14:71608600-71610600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr14:71608600-71610800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr14:71608600-71610800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr14:71608600-71611000	Enhancers	Dnd41	blood
43	chr14:71608800-71610000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr14:71608800-71610200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:71608800-71610400	Enhancers	HUVEC	blood vessel
46	chr14:71608800-71610600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:71608800-71610600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr14:71608800-71610800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr14:71608800-71610800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr14:71609000-71609800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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