Variant report

Variant	rs36559
Chromosome Location	chr14:71354949-71354950
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71315330..71318187-chr14:71353000..71355911,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17108808	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17108862	0.81[AMR][1000 genomes]
rs2158996	0.81[AMR][1000 genomes]
rs2240533	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs2526850	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526851	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526854	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526857	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526858	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526868	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2526872	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526879	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2810075	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2810096	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2810097	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2810099	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2810104	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2810105	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2810114	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36555	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36567	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829954	0.83[AMR][1000 genomes]
rs56306703	0.81[AMR][1000 genomes]
rs61990379	0.81[AMR][1000 genomes]
rs61990387	0.81[AMR][1000 genomes]
rs8010063	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs8014273	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs989501	0.93[ASW][hapmap]

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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs36559	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs36559	PCNX	cis	Nerve Tibial	GTEx
rs36559	PCNX	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71349800-71356000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr14:71349800-71356200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr14:71350000-71356200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr14:71350600-71355600	Enhancers	Primary B cells from cord blood	blood
5	chr14:71350600-71356600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr14:71350600-71373000	Weak transcription	Spleen	Spleen
7	chr14:71351000-71355000	Flanking Active TSS	GM12878-XiMat	blood
8	chr14:71351200-71357400	Enhancers	Fetal Thymus	thymus
9	chr14:71351800-71356000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:71351800-71361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr14:71351800-71365200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:71352200-71355600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:71352200-71355800	Enhancers	Primary T cells from cord blood	blood
14	chr14:71352800-71355000	Enhancers	Primary B cells from peripheral blood	blood
15	chr14:71353000-71355000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr14:71353200-71365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr14:71353400-71355000	Enhancers	Colon Smooth Muscle	Colon
18	chr14:71353400-71355200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr14:71353400-71355400	Enhancers	NH-A	brain
20	chr14:71353400-71355600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr14:71353400-71355600	Enhancers	Hela-S3	cervix
22	chr14:71353600-71355600	Enhancers	Fetal Stomach	stomach
23	chr14:71353600-71356600	Enhancers	NHLF	lung
24	chr14:71353600-71356800	Enhancers	HMEC	breast
25	chr14:71353600-71360800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:71353800-71355400	Enhancers	NHEK	skin
27	chr14:71353800-71356000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:71353800-71356600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr14:71353800-71357400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr14:71354000-71355200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr14:71354000-71356000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr14:71354000-71356000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr14:71354000-71356400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr14:71354000-71360000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr14:71354200-71355000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr14:71354200-71355000	Flanking Active TSS	Osteobl	bone
37	chr14:71354200-71356600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:71354200-71356600	Enhancers	HSMMtube	muscle
39	chr14:71354200-71356800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr14:71354400-71355000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr14:71354400-71356200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr14:71354400-71356200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr14:71354400-71356200	Enhancers	HSMM	muscle
44	chr14:71354400-71356600	Enhancers	Primary hematopoietic stem cells	blood
45	chr14:71354400-71359600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr14:71354400-71359800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr14:71354600-71355000	Enhancers	Aorta	Aorta
48	chr14:71354600-71355000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr14:71354600-71355600	Enhancers	Small Intestine	intestine
50	chr14:71354600-71356000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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