Variant report

Variant	rs62052890
Chromosome Location	chr16:72556048-72556049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PMFBP1-4	chr16:72556037-72556522	ENSG00000261008.2

Extended variants
information (count: 179 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs1001493	0.89[EUR][1000 genomes]
rs1006805	0.94[EUR][1000 genomes]
rs10468266	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10492821	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10492822	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11641842	0.89[EUR][1000 genomes]
rs11643203	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11860023	0.90[EUR][1000 genomes]
rs12051542	0.94[EUR][1000 genomes]
rs12325146	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12325151	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12445443	0.91[EUR][1000 genomes]
rs12596611	0.90[EUR][1000 genomes]
rs12599375	0.93[EUR][1000 genomes]
rs12708933	0.81[EUR][1000 genomes]
rs1297137	0.84[ASN][1000 genomes]
rs13333122	0.93[EUR][1000 genomes]
rs13335806	0.90[EUR][1000 genomes]
rs1429071	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1429072	0.93[EUR][1000 genomes]
rs1560278	0.87[EUR][1000 genomes]
rs16970933	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16971030	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16971035	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16971036	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16971037	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16971050	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16971112	0.91[EUR][1000 genomes]
rs16971114	0.87[EUR][1000 genomes]
rs17287903	0.92[EUR][1000 genomes]
rs17359949	0.92[EUR][1000 genomes]
rs17608394	0.91[ASN][1000 genomes]
rs17609544	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17609577	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17609787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609808	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17669912	0.81[ASN][1000 genomes]
rs17676691	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17676709	0.91[ASN][1000 genomes]
rs17677146	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17677484	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17677616	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17677890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17841357	0.91[EUR][1000 genomes]
rs1864229	0.91[EUR][1000 genomes]
rs2163068	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2262554	0.84[ASN][1000 genomes]
rs2336437	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2358801	0.90[EUR][1000 genomes]
rs2905697	0.93[EUR][1000 genomes]
rs2905699	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2914774	0.93[EUR][1000 genomes]
rs2914777	0.91[EUR][1000 genomes]
rs2914779	0.95[EUR][1000 genomes]
rs2967232	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2967233	0.92[EUR][1000 genomes]
rs2967234	0.91[EUR][1000 genomes]
rs2967240	0.89[EUR][1000 genomes]
rs35005335	0.87[EUR][1000 genomes]
rs4788473	0.87[EUR][1000 genomes]
rs55766519	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55808336	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56323671	0.93[EUR][1000 genomes]
rs56347149	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56348767	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56389222	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56404261	0.90[EUR][1000 genomes]
rs57220817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57755001	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58549165	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58745414	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58770834	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58860566	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59966262	0.87[ASN][1000 genomes]
rs60502114	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60855478	0.85[ASN][1000 genomes]
rs61475520	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62051129	0.90[ASN][1000 genomes]
rs62051130	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62051131	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62051136	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62051137	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62051145	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62051146	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62051147	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62051148	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62051149	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62051150	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62051151	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62051486	0.92[EUR][1000 genomes]
rs62051488	0.92[EUR][1000 genomes]
rs62051497	0.86[EUR][1000 genomes]
rs62051500	0.82[EUR][1000 genomes]
rs62052871	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62052877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62052878	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62052879	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052880	0.91[EUR][1000 genomes]
rs62052881	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052888	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62052891	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62052894	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62052895	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62052909	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62052911	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62052915	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62052920	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62052921	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62052923	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62052927	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62052954	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62053968	0.81[ASN][1000 genomes]
rs62053991	0.85[ASN][1000 genomes]
rs62053995	0.84[ASN][1000 genomes]
rs62053996	0.83[ASN][1000 genomes]
rs62053997	0.84[ASN][1000 genomes]
rs62053998	0.85[ASN][1000 genomes]
rs62054469	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62054470	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7188640	0.86[EUR][1000 genomes]
rs7189331	0.87[EUR][1000 genomes]
rs7192221	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7193177	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7194024	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7194470	0.90[EUR][1000 genomes]
rs7195825	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7198233	0.84[EUR][1000 genomes]
rs7198431	0.88[EUR][1000 genomes]
rs7198449	0.85[ASN][1000 genomes]
rs7198788	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7199954	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7199970	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7200814	0.85[ASN][1000 genomes]
rs7204260	0.83[ASN][1000 genomes]
rs7205109	0.86[EUR][1000 genomes]
rs7205716	0.84[ASN][1000 genomes]
rs7206298	0.87[ASN][1000 genomes]
rs72791149	0.87[ASN][1000 genomes]
rs72793244	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72793252	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72793263	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72793266	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72793271	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8044665	0.82[EUR][1000 genomes]
rs8046749	0.93[EUR][1000 genomes]
rs8048181	0.80[EUR][1000 genomes]
rs8048832	0.80[EUR][1000 genomes]
rs8049577	0.92[EUR][1000 genomes]
rs8050815	0.93[EUR][1000 genomes]
rs8056067	0.81[ASN][1000 genomes]
rs8058832	0.81[ASN][1000 genomes]
rs8063172	0.81[ASN][1000 genomes]
rs8064129	0.90[EUR][1000 genomes]
rs806732	0.85[ASN][1000 genomes]
rs806733	0.85[ASN][1000 genomes]
rs806738	0.90[ASN][1000 genomes]
rs806747	0.84[ASN][1000 genomes]
rs877641	0.90[EUR][1000 genomes]
rs9922217	0.93[EUR][1000 genomes]
rs9924296	0.90[EUR][1000 genomes]
rs9925470	0.85[EUR][1000 genomes]
rs9940600	0.83[EUR][1000 genomes]
rs999697	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs999698	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1055807	chr16:72418417-72614308	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv523524	chr16:72464460-72635674	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1055142	chr16:72473520-72627783	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv542950	chr16:72473520-72627783	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv530712	chr16:72499171-72744114	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1064928	chr16:72509626-72627783	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1065173	chr16:72509626-72693970	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv542951	chr16:72509626-72693970	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv518234	chr16:72544447-72635674	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72545000-72588800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr16:72549200-72556200	Weak transcription	Esophagus	oesophagus
3	chr16:72552600-72567400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:72554400-72556400	Weak transcription	HSMM	muscle
5	chr16:72554600-72571400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:72554800-72557400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:72555200-72557200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:72555200-72557800	Weak transcription	K562	blood
9	chr16:72555400-72556200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr16:72555400-72557400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr16:72555400-72558000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr16:72555600-72556400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr16:72555600-72556800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr16:72555600-72557200	ZNF genes & repeats	Dnd41	blood
15	chr16:72555600-72557600	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr16:72555600-72557800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr16:72555800-72556200	Weak transcription	Fetal Thymus	thymus
18	chr16:72555800-72556200	Weak transcription	Thymus	Thymus
19	chr16:72555800-72556800	ZNF genes & repeats	HepG2	liver
20	chr16:72555800-72557400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
21	chr16:72555800-72557400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr16:72556000-72556600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr16:72556000-72556600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr16:72556000-72557400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:72556000-72557600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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