Variant report

Variant	rs72808985
Chromosome Location	chr5:115705841-115705842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115704428..115706706-chr5:115709540..115711421,2	MCF-7	breast:

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: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10519452	1.00[AFR][1000 genomes]
rs17139251	1.00[AFR][1000 genomes]
rs17139524	0.90[AMR][1000 genomes]
rs17139604	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17139607	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55857351	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56168251	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57209700	0.91[EUR][1000 genomes]
rs57526524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58291729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58776100	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72804900	1.00[AFR][1000 genomes]
rs72806907	1.00[AFR][1000 genomes]
rs72806917	1.00[AFR][1000 genomes]
rs72806927	1.00[AFR][1000 genomes]
rs72806930	1.00[AFR][1000 genomes]
rs72806931	1.00[AFR][1000 genomes]
rs72806933	1.00[AFR][1000 genomes]
rs72808912	1.00[AFR][1000 genomes]
rs72808927	1.00[AFR][1000 genomes]
rs72808929	1.00[AFR][1000 genomes]
rs72808932	1.00[AFR][1000 genomes]
rs72808949	1.00[AFR][1000 genomes]
rs72808969	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72808973	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72808976	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72808977	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72808978	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72808979	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808981	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72808984	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72808987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72808989	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72808992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115685000-115721400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr5:115687200-115706400	Weak transcription	Liver	Liver
3	chr5:115694400-115707800	Weak transcription	Spleen	Spleen
4	chr5:115695800-115706600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr5:115695800-115714600	Weak transcription	Thymus	Thymus
6	chr5:115696000-115708000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:115696400-115707600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr5:115696400-115708400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:115697600-115707400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:115697600-115708200	Weak transcription	Lung	lung
11	chr5:115697600-115712000	Weak transcription	Aorta	Aorta
12	chr5:115697600-115714000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:115697600-115748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:115697800-115706600	Weak transcription	Fetal Intestine Small	intestine
15	chr5:115697800-115706800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:115697800-115708200	Weak transcription	Psoas Muscle	Psoas
17	chr5:115697800-115708400	Weak transcription	Colonic Mucosa	Colon
18	chr5:115698000-115722800	Weak transcription	Pancreas	Pancrea
19	chr5:115698400-115714000	Weak transcription	Right Ventricle	heart
20	chr5:115699400-115710200	Weak transcription	Primary B cells from cord blood	blood
21	chr5:115701400-115706200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:115702800-115706000	Weak transcription	Fetal Kidney	kidney
23	chr5:115705200-115706800	Enhancers	K562	blood
24	chr5:115705200-115707400	Enhancers	Primary T cells from cord blood	blood
25	chr5:115705200-115713000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:115705400-115706000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr5:115705400-115706200	Enhancers	Fetal Thymus	thymus
28	chr5:115705400-115706600	Enhancers	HUVEC	blood vessel
29	chr5:115705400-115706800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr5:115705400-115707200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:115705600-115706000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:115705600-115706000	Enhancers	Right Atrium	heart
33	chr5:115705600-115706200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:115705600-115706800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr5:115705600-115707200	Weak transcription	Adipose Nuclei	Adipose
36	chr5:115705600-115707400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:115705600-115708200	Weak transcription	Esophagus	oesophagus
38	chr5:115705800-115706000	Enhancers	Fetal Muscle Leg	muscle
39	chr5:115705800-115706200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr5:115705800-115707000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr5:115705800-115707200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr5:115705800-115708200	Weak transcription	Left Ventricle	heart

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