Variant report

Variant	rs56947773
Chromosome Location	chr5:115703577-115703578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEMA6A-1	chr5:115703287-115706170	ENSG00000249280
2	lnc-SEMA6A-1	chr5:115703113-115706170	NONHSAT103361

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10519460	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1073205	0.84[EUR][1000 genomes]
rs11948686	1.00[EUR][1000 genomes]
rs11949705	1.00[ASN][1000 genomes]
rs11956927	0.84[EUR][1000 genomes]
rs17139530	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17139552	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17139556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17139565	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17139591	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4920914	1.00[EUR][1000 genomes]
rs4921092	0.84[EUR][1000 genomes]
rs4921093	0.84[EUR][1000 genomes]
rs4921095	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55702251	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55817922	0.84[EUR][1000 genomes]
rs57067978	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57362825	0.92[EUR][1000 genomes]
rs59570866	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59951603	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6594964	1.00[EUR][1000 genomes]
rs6594965	1.00[EUR][1000 genomes]
rs6874012	0.84[EUR][1000 genomes]
rs6878067	0.92[ASN][1000 genomes]
rs6893952	0.84[EUR][1000 genomes]
rs712590	0.84[EUR][1000 genomes]
rs73263060	0.84[EUR][1000 genomes]
rs73264968	1.00[EUR][1000 genomes]
rs73266811	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73781050	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7705979	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7716629	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7716923	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7727761	0.92[ASN][1000 genomes]
rs7734398	0.84[EUR][1000 genomes]
rs7737229	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2763489	chr5:115693166-115733327	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115684400-115705800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr5:115685000-115721400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:115687200-115706400	Weak transcription	Liver	Liver
4	chr5:115694400-115707800	Weak transcription	Spleen	Spleen
5	chr5:115695800-115706600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:115695800-115714600	Weak transcription	Thymus	Thymus
7	chr5:115696000-115708000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr5:115696400-115707600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:115696400-115708400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:115697600-115705400	Weak transcription	Left Ventricle	heart
11	chr5:115697600-115707400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr5:115697600-115708200	Weak transcription	Lung	lung
13	chr5:115697600-115712000	Weak transcription	Aorta	Aorta
14	chr5:115697600-115714000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:115697600-115748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:115697800-115706600	Weak transcription	Fetal Intestine Small	intestine
17	chr5:115697800-115706800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:115697800-115708200	Weak transcription	Psoas Muscle	Psoas
19	chr5:115697800-115708400	Weak transcription	Colonic Mucosa	Colon
20	chr5:115698000-115722800	Weak transcription	Pancreas	Pancrea
21	chr5:115698400-115705400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr5:115698400-115714000	Weak transcription	Right Ventricle	heart
23	chr5:115699000-115705200	Weak transcription	Primary T cells from cord blood	blood
24	chr5:115699400-115710200	Weak transcription	Primary B cells from cord blood	blood
25	chr5:115701400-115705200	Weak transcription	K562	blood
26	chr5:115701400-115706200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:115702800-115706000	Weak transcription	Fetal Kidney	kidney

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