Variant report

Variant	rs778693
Chromosome Location	chr7:65872345-65872346
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GUSB-10	chr7:65872277-65872351	NONHSAT121176

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10247526	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10807701	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10807702	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10950032	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12530490	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1267816	1.00[AFR][1000 genomes]
rs1267819	1.00[AFR][1000 genomes]
rs1267820	1.00[AFR][1000 genomes]
rs13222887	1.00[AFR][1000 genomes]
rs13224048	1.00[AFR][1000 genomes]
rs13232193	0.87[AFR][1000 genomes]
rs13235972	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13237037	1.00[AFR][1000 genomes]
rs13237344	0.95[AFR][1000 genomes]
rs13241548	1.00[AFR][1000 genomes]
rs13242216	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1392104	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1499613	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1499614	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1532573	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1553174	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1796215	1.00[AFR][1000 genomes]
rs1796220	1.00[AFR][1000 genomes]
rs1796228	1.00[AFR][1000 genomes]
rs1979823	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2460426	0.86[AFR][1000 genomes]
rs2533288	0.95[AFR][1000 genomes]
rs2707831	1.00[AFR][1000 genomes]
rs2707844	0.95[AFR][1000 genomes]
rs34192067	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34363376	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34700450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34807232	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35261784	0.82[AFR][1000 genomes]
rs35823062	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35825036	0.90[AFR][1000 genomes]
rs36104268	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4149468	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4481472	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4718317	0.86[AFR][1000 genomes]
rs4718333	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58668827	1.00[AFR][1000 genomes]
rs58669269	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66630579	0.85[AFR][1000 genomes]
rs6958289	0.86[AFR][1000 genomes]
rs6958420	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6964245	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6964530	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71563118	0.95[AFR][1000 genomes]
rs7778911	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs778679	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778683	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778687	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778698	0.93[ASN][1000 genomes]
rs778701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778704	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778717	0.89[ASN][1000 genomes]
rs778718	0.84[AMR][1000 genomes]
rs778729	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778732	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778733	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7792391	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7804223	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7808834	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS 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	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv981506	chr7:65842694-65876873	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs778693	RP4-756H11.3	cis	lung	GTEx
rs778693	ASL	cis	multi-tissue	Pritchard
rs778693	VKORC1L1	cis	Whole Blood	GTEx
rs778693	GUSB	cis	Whole Blood	GTEx
rs778693	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65840000-65878400	Weak transcription	Psoas Muscle	Psoas
2	chr7:65840400-65873400	Weak transcription	K562	blood
3	chr7:65841400-65875400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:65843400-65877600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:65843600-65878200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:65844000-65878400	Weak transcription	Thymus	Thymus
7	chr7:65845000-65873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:65845000-65873600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:65845000-65878000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:65845000-65878000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr7:65845000-65878200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:65845000-65878200	Weak transcription	Right Ventricle	heart
13	chr7:65845000-65878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:65845000-65878400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:65845000-65878400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:65845200-65873400	Weak transcription	HepG2	liver
17	chr7:65845200-65878200	Weak transcription	Left Ventricle	heart
18	chr7:65845200-65878600	Weak transcription	Aorta	Aorta
19	chr7:65845400-65875400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:65845400-65877200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:65845400-65878000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr7:65845400-65878200	Weak transcription	Brain Germinal Matrix	brain
23	chr7:65845400-65878200	Weak transcription	Pancreas	Pancrea
24	chr7:65845600-65873400	Weak transcription	Ovary	ovary
25	chr7:65845600-65877400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr7:65845600-65878200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:65845600-65878200	Weak transcription	Fetal Thymus	thymus
28	chr7:65845600-65878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:65845600-65878600	Weak transcription	Gastric	stomach
30	chr7:65846200-65875400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:65846200-65878200	Weak transcription	Fetal Lung	lung
32	chr7:65847800-65878400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:65850800-65878200	Weak transcription	Lung	lung
34	chr7:65854800-65878400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr7:65858600-65874400	Weak transcription	GM12878-XiMat	blood
36	chr7:65858600-65878200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:65858800-65876400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:65861000-65878600	Weak transcription	HSMM	muscle
39	chr7:65861600-65873200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:65861800-65878400	Weak transcription	HSMMtube	muscle
41	chr7:65861800-65880800	Weak transcription	Hela-S3	cervix
42	chr7:65863000-65878000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:65863000-65878200	Weak transcription	Fetal Brain Male	brain
44	chr7:65863400-65875000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr7:65863400-65878400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:65863600-65876200	Strong transcription	Liver	Liver
47	chr7:65863800-65878000	Weak transcription	Brain Angular Gyrus	brain
48	chr7:65863800-65878200	Weak transcription	Colonic Mucosa	Colon
49	chr7:65864400-65872400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr7:65864600-65878200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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