Variant report

Variant	rs2810099
Chromosome Location	chr14:71432421-71432422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1012725	0.81[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs12100737	0.88[ASW][hapmap];0.83[TSI][hapmap]
rs17093738	0.84[AMR][1000 genomes]
rs17108804	0.88[ASW][hapmap];0.83[TSI][hapmap]
rs17108808	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108862	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17109053	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2158996	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2158997	0.88[ASW][hapmap];0.83[TSI][hapmap]
rs2240533	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.85[AMR][1000 genomes]
rs2526850	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526851	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526854	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526857	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526858	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526868	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap]
rs2526872	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526877	0.88[ASW][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs2526879	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2810073	0.88[ASW][hapmap];0.83[TSI][hapmap]
rs2810075	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810097	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810098	0.88[ASW][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs2810100	0.81[AMR][1000 genomes]
rs2810104	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810105	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810114	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36555	0.94[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36559	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs36567	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3814871	0.88[ASW][hapmap];0.83[TSI][hapmap]
rs3829954	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56043821	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56306703	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59699904	0.84[AMR][1000 genomes]
rs61990379	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61990380	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61990387	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61992065	0.82[AMR][1000 genomes]
rs6573993	0.82[ASN][1000 genomes]
rs67188216	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8007026	0.88[ASW][hapmap];0.85[TSI][hapmap]
rs8010063	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8013146	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8014273	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8181986	0.84[AMR][1000 genomes]
rs917065	0.88[ASW][hapmap];0.83[TSI][hapmap]

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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2810099	PCNX	cis	lymphoblastoid	seeQTL
rs2810099	PCNX	cis	Thyroid	GTEx
rs2810099	PCNX	cis	Artery Tibial	GTEx
rs2810099	PCNX	cis	Nerve Tibial	GTEx
rs2810099	PCNX	cis	Artery Aorta	GTEx
rs2810099	PCNX	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr14:71411000-71443200	Weak transcription	Hela-S3	cervix
4	chr14:71411000-71443600	Weak transcription	NHLF	lung
5	chr14:71411000-71443800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr14:71411000-71443800	Weak transcription	Gastric	stomach
7	chr14:71411400-71444000	Weak transcription	Brain Angular Gyrus	brain
8	chr14:71411800-71444200	Weak transcription	Fetal Brain Male	brain
9	chr14:71414000-71433000	Weak transcription	NHEK	skin
10	chr14:71414400-71443400	Weak transcription	Fetal Kidney	kidney
11	chr14:71414800-71436800	Weak transcription	Fetal Brain Female	brain
12	chr14:71414800-71438800	Weak transcription	Small Intestine	intestine
13	chr14:71414800-71443600	Weak transcription	Brain Hippocampus Middle	brain
14	chr14:71414800-71443600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:71414800-71443800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr14:71414800-71443800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr14:71415000-71435600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr14:71415000-71436000	Weak transcription	Brain Germinal Matrix	brain
19	chr14:71415000-71436000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr14:71415000-71436200	Weak transcription	Fetal Muscle Leg	muscle
21	chr14:71415000-71436200	Weak transcription	Ovary	ovary
22	chr14:71415000-71436400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:71415000-71443200	Weak transcription	Spleen	Spleen
24	chr14:71415000-71443400	Weak transcription	Esophagus	oesophagus
25	chr14:71415000-71443600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr14:71415000-71443600	Weak transcription	Aorta	Aorta
27	chr14:71415000-71443600	Weak transcription	Lung	lung
28	chr14:71415000-71443600	Weak transcription	Pancreas	Pancrea
29	chr14:71415000-71443800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr14:71415200-71434600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr14:71416600-71435800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:71416600-71443600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr14:71416600-71443600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:71416800-71433000	Weak transcription	NHDF-Ad	bronchial
35	chr14:71416800-71436000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr14:71416800-71436200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:71419400-71434400	Weak transcription	Placenta	Placenta
38	chr14:71420000-71434600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:71420000-71436400	Weak transcription	Fetal Intestine Small	intestine
40	chr14:71420800-71436200	Weak transcription	Left Ventricle	heart
41	chr14:71422600-71436000	Weak transcription	Osteobl	bone
42	chr14:71422600-71442600	Weak transcription	A549	lung
43	chr14:71422800-71433600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr14:71422800-71435600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr14:71423000-71443800	Weak transcription	Brain Anterior Caudate	brain
46	chr14:71423200-71432600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr14:71423200-71444400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:71423400-71433200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr14:71423400-71435600	Weak transcription	Adipose Nuclei	Adipose
50	chr14:71423400-71436400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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