Variant report

Variant	rs5744720
Chromosome Location	chr5:74894333-74894334
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POC5-1	chr5:74894307-74894806	ENSG00000248881.1

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11948350	0.94[EUR][1000 genomes]
rs11948442	0.94[EUR][1000 genomes]
rs11952534	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11953173	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11953883	0.94[EUR][1000 genomes]
rs11955568	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11955819	0.94[EUR][1000 genomes]
rs11956111	0.94[EUR][1000 genomes]
rs11956112	0.94[EUR][1000 genomes]
rs11956755	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11960741	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11960747	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11960771	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1422441	0.94[EUR][1000 genomes]
rs1489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872590	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16872661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872677	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16872683	0.94[EUR][1000 genomes]
rs16872693	0.94[EUR][1000 genomes]
rs1991450	0.94[EUR][1000 genomes]
rs2112348	0.94[EUR][1000 genomes]
rs2112349	0.89[EUR][1000 genomes]
rs2112350	0.94[EUR][1000 genomes]
rs4640773	0.88[EUR][1000 genomes]
rs56832737	0.94[EUR][1000 genomes]
rs57414757	0.94[EUR][1000 genomes]
rs5744617	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57531042	0.94[EUR][1000 genomes]
rs57670471	0.94[EUR][1000 genomes]
rs58216239	0.94[EUR][1000 genomes]
rs59427628	0.94[EUR][1000 genomes]
rs60385047	0.94[EUR][1000 genomes]
rs60609097	0.94[EUR][1000 genomes]
rs61516153	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865606	0.94[EUR][1000 genomes]
rs6866607	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6870090	0.94[EUR][1000 genomes]
rs6882452	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6894068	0.94[EUR][1000 genomes]
rs6895148	0.94[EUR][1000 genomes]
rs6898308	0.82[EUR][1000 genomes]
rs73120804	0.94[EUR][1000 genomes]
rs73120805	0.94[EUR][1000 genomes]
rs73120807	0.94[EUR][1000 genomes]
rs73120811	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73120822	0.94[EUR][1000 genomes]
rs73120824	0.94[EUR][1000 genomes]
rs73120848	1.00[EUR][1000 genomes]
rs73120849	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73120850	1.00[EUR][1000 genomes]
rs73122744	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122755	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122770	0.94[EUR][1000 genomes]
rs73122771	0.94[EUR][1000 genomes]
rs73122772	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73124734	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73124747	0.94[EUR][1000 genomes]
rs73124750	0.94[EUR][1000 genomes]
rs7722940	0.82[EUR][1000 genomes]
rs7724771	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	esv3373419	chr5:74894212-74894410	Weak transcription Strong transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74818200-74897400	Weak transcription	Thymus	Thymus
2	chr5:74822800-74896000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr5:74833400-74906800	Weak transcription	Brain Substantia Nigra	brain
4	chr5:74839400-74897400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:74841200-74899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:74850200-74896200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:74862200-74897800	Weak transcription	Brain Germinal Matrix	brain
8	chr5:74862600-74897200	Weak transcription	Lung	lung
9	chr5:74862800-74897400	Weak transcription	Pancreas	Pancrea
10	chr5:74862800-74897400	Weak transcription	Spleen	Spleen
11	chr5:74862800-74897600	Weak transcription	Gastric	stomach
12	chr5:74862800-74907200	Weak transcription	Esophagus	oesophagus
13	chr5:74863000-74896200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:74863600-74905800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:74863800-74906800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:74864000-74897400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:74864000-74897400	Weak transcription	NHEK	skin
18	chr5:74864000-74899600	Weak transcription	Hela-S3	cervix
19	chr5:74864000-74907000	Weak transcription	Psoas Muscle	Psoas
20	chr5:74865800-74906800	Weak transcription	Colonic Mucosa	Colon
21	chr5:74867600-74907200	Weak transcription	Small Intestine	intestine
22	chr5:74871400-74897400	Weak transcription	Aorta	Aorta
23	chr5:74871400-74897400	Weak transcription	Brain Angular Gyrus	brain
24	chr5:74871400-74897400	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:74871400-74897400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:74871800-74900600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:74872400-74898400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:74873600-74907000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:74873800-74899200	Weak transcription	K562	blood
30	chr5:74873800-74901000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:74874600-74897400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:74875200-74907000	Weak transcription	Right Ventricle	heart
33	chr5:74875800-74903400	Weak transcription	Fetal Thymus	thymus
34	chr5:74877000-74898400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:74877400-74896200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:74877400-74899200	Weak transcription	HUVEC	blood vessel
37	chr5:74878200-74899000	Weak transcription	HMEC	breast
38	chr5:74878400-74898200	Weak transcription	Fetal Brain Male	brain
39	chr5:74878600-74901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:74879000-74907000	Weak transcription	HepG2	liver
41	chr5:74879600-74897800	Weak transcription	NHLF	lung
42	chr5:74881400-74895800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:74881800-74896800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:74882400-74897000	Weak transcription	Fetal Lung	lung
45	chr5:74884600-74901200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:74884800-74897200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:74884800-74897800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:74885000-74897800	Weak transcription	NH-A	brain
49	chr5:74885400-74901000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:74887800-74895800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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