Variant report

Variant	rs61990419
Chromosome Location	chr14:71536287-71536288
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1018977	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12100737	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12101246	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883437	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12892739	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12896370	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12897533	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17108804	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108822	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17108862	0.80[AMR][1000 genomes]
rs17108877	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17108925	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108967	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs183404	0.80[ASN][1000 genomes]
rs1859468	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2010061	0.87[AMR][1000 genomes]
rs2097866	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2158996	0.80[AMR][1000 genomes]
rs2158997	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2189806	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs221899	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs221902	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs221903	0.87[ASN][1000 genomes]
rs221907	0.87[ASN][1000 genomes]
rs221909	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221912	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221920	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs221921	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221922	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs221923	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs221927	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286310	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2332477	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526846	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526852	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2526855	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526860	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2526862	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526874	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2526876	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2526877	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526878	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2526882	0.84[AMR][1000 genomes]
rs2526886	0.84[AMR][1000 genomes]
rs2526890	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810071	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2810073	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2810098	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810100	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810107	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810115	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2810116	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2810117	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28374308	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34049963	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34093157	0.81[EUR][1000 genomes]
rs34257131	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34368938	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34488204	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34731365	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34763296	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35631530	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814869	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814871	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4048474	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132849	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4391999	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4426283	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56021283	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56306703	0.80[AMR][1000 genomes]
rs58133478	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58984901	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990379	0.80[AMR][1000 genomes]
rs61990387	0.80[AMR][1000 genomes]
rs67981189	0.93[AMR][1000 genomes]
rs7145484	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7146591	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7146932	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7153237	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7157250	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003103	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8003227	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8007026	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8010063	0.80[AMR][1000 genomes]
rs8012728	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8014273	0.80[AMR][1000 genomes]
rs8016506	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8022768	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs917065	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs989501	0.80[AMR][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	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
11	esv3430065	chr14:71534649-71536547	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs61990419	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs61990419	PCNX	cis	Nerve Tibial	GTEx
rs61990419	PCNX	cis	Thyroid	GTEx
rs61990419	PCNX	cis	Artery Aorta	GTEx
rs61990419	PCNX	cis	Artery Tibial	GTEx
rs61990419	PCNX	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71495800-71546200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71497000-71554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:71499600-71540800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:71510200-71538200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:71511600-71540800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr14:71511600-71541000	Weak transcription	Pancreas	Pancrea
7	chr14:71518200-71544000	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr14:71525800-71539800	Weak transcription	Brain Substantia Nigra	brain
9	chr14:71527400-71540000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:71527600-71540000	Weak transcription	Brain Angular Gyrus	brain
11	chr14:71528000-71541200	Weak transcription	Small Intestine	intestine
12	chr14:71528000-71543200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr14:71528200-71539000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:71528400-71539800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:71528400-71540800	Weak transcription	HSMMtube	muscle
16	chr14:71528400-71541200	Weak transcription	Right Ventricle	heart
17	chr14:71528600-71536400	Weak transcription	Fetal Brain Male	brain
18	chr14:71528600-71536400	Weak transcription	NHLF	lung
19	chr14:71528600-71536600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr14:71528600-71537600	Weak transcription	Gastric	stomach
21	chr14:71528600-71539800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:71528600-71539800	Weak transcription	Placenta	Placenta
23	chr14:71528600-71539800	Weak transcription	Lung	lung
24	chr14:71528600-71540000	Weak transcription	Fetal Thymus	thymus
25	chr14:71528600-71540200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:71528600-71540200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr14:71528600-71540200	Weak transcription	Aorta	Aorta
28	chr14:71528600-71540200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr14:71528600-71540200	Weak transcription	Esophagus	oesophagus
30	chr14:71528600-71540800	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:71528600-71540800	Weak transcription	A549	lung
32	chr14:71528600-71543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:71528800-71540000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr14:71528800-71540200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr14:71528800-71540200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr14:71528800-71540200	Weak transcription	Hela-S3	cervix
37	chr14:71528800-71540200	Weak transcription	HepG2	liver
38	chr14:71529000-71539600	Weak transcription	Fetal Stomach	stomach
39	chr14:71529000-71539600	Weak transcription	HUVEC	blood vessel
40	chr14:71529000-71539800	Weak transcription	Spleen	Spleen
41	chr14:71529000-71540200	Weak transcription	Thymus	Thymus
42	chr14:71529000-71543000	Weak transcription	Psoas Muscle	Psoas
43	chr14:71529200-71540200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr14:71529600-71538200	Weak transcription	Fetal Heart	heart
45	chr14:71529800-71537600	Weak transcription	Ovary	ovary
46	chr14:71530000-71541000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr14:71530200-71536400	Weak transcription	NHEK	skin
48	chr14:71530400-71536400	Weak transcription	NHDF-Ad	bronchial
49	chr14:71530800-71536400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr14:71531400-71536400	Weak transcription	GM12878-XiMat	blood

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