Variant report

Variant	rs13224048
Chromosome Location	chr7:65993766-65993767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VKORC1L1-2	chr7:65993448-65996860	ENSG00000249705
2	lnc-SBDS-4	chr7:65993425-65996858	ENSG00000229180
3	lnc-SBDS-4	chr7:65992918-65996858	NONHSAT121200
4	lnc-SBDS-4	chr7:65991075-65996858	ENSG00000229180.4

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10247526	0.90[AFR][1000 genomes]
rs10807702	0.90[AFR][1000 genomes]
rs1267816	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267817	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1267818	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1267819	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267820	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12698542	1.00[AFR][1000 genomes]
rs13222887	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13232193	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13235972	1.00[AFR][1000 genomes]
rs13237037	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13237344	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13241548	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1392104	0.82[AFR][1000 genomes]
rs1618893	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1638731	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1638734	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1638736	0.83[ASN][1000 genomes]
rs1796215	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796220	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796228	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1882655	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1922723	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2141924	1.00[AFR][1000 genomes]
rs2178742	1.00[AFR][1000 genomes]
rs2420609	0.99[ASN][1000 genomes]
rs2533287	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2533288	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659903	1.00[AFR][1000 genomes]
rs2659911	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2659913	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2707823	1.00[AFR][1000 genomes]
rs2707826	0.91[AFR][1000 genomes]
rs2707828	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2707830	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2707831	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2707832	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2707833	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2707838	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2707840	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2707844	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34073431	0.94[ASN][1000 genomes]
rs34192067	1.00[AFR][1000 genomes]
rs34363376	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34700450	1.00[AFR][1000 genomes]
rs34807232	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35261784	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35370033	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35823062	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35825036	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36104268	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3936	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718333	0.90[AFR][1000 genomes]
rs58668827	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58669269	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60326618	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6460312	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs66630579	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71563118	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73135918	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73150635	0.98[ASN][1000 genomes]
rs778679	0.91[AFR][1000 genomes]
rs778683	0.91[AFR][1000 genomes]
rs778687	0.83[AFR][1000 genomes]
rs778691	1.00[AFR][1000 genomes]
rs778693	1.00[AFR][1000 genomes]
rs778701	1.00[AFR][1000 genomes]
rs778704	1.00[AFR][1000 genomes]
rs778729	0.82[AFR][1000 genomes]
rs778732	0.90[AFR][1000 genomes]
rs778733	0.82[AFR][1000 genomes]
rs7792391	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv3447484	chr7:65909457-66033145	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv888327	chr7:65938980-66029429	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	nsv967444	chr7:65992587-66013934	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13224048	GUSB	cis	Whole Blood	GTEx
rs13224048	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs13224048	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13224048	VKORC1L1	cis	Whole Blood	GTEx
rs13224048	RP4-756H11.3	cis	lung	GTEx
rs13224048	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13224048	ASL	cis	multi-tissue	Pritchard

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65981400-66001000	Weak transcription	Fetal Brain Female	brain
2	chr7:65983400-66001800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr7:65983400-66006000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:65983600-65994400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:65983600-66000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:65985600-65994600	Weak transcription	Spleen	Spleen
7	chr7:65985800-66006200	Weak transcription	Pancreas	Pancrea
8	chr7:65986400-65994600	Weak transcription	HepG2	liver
9	chr7:65987400-65994800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:65987600-65994400	Weak transcription	Right Ventricle	heart
11	chr7:65987800-65995000	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:65987800-66006200	Weak transcription	Gastric	stomach
13	chr7:65988000-65993800	Weak transcription	Ovary	ovary
14	chr7:65988000-65995000	Weak transcription	Brain Angular Gyrus	brain
15	chr7:65988200-65994400	Weak transcription	Brain Anterior Caudate	brain
16	chr7:65988400-65993800	Weak transcription	Primary T cells from cord blood	blood
17	chr7:65988400-65994400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:65988400-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:65988600-66006200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr7:65988600-66009000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:65988600-66009000	Weak transcription	HSMMtube	muscle
22	chr7:65988800-65994600	Weak transcription	NHLF	lung
23	chr7:65988800-65996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:65988800-66008200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:65989000-66006200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:65989000-66007600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:65989400-65996800	Strong transcription	Fetal Stomach	stomach
28	chr7:65989400-65998800	Weak transcription	Right Atrium	heart
29	chr7:65989600-65996400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:65989600-65997000	Strong transcription	Fetal Intestine Small	intestine
31	chr7:65989800-65993800	Weak transcription	Fetal Intestine Large	intestine
32	chr7:65989800-65994400	Weak transcription	Aorta	Aorta
33	chr7:65989800-65994800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr7:65989800-65995000	Weak transcription	Placenta	Placenta
35	chr7:65989800-66004200	Weak transcription	Dnd41	blood
36	chr7:65990000-66009000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr7:65990600-65994400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:65990600-65994400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:65990600-66004000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr7:65990600-66005600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:65991200-66009800	Weak transcription	Small Intestine	intestine
42	chr7:65991400-65994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:65991400-66006200	Weak transcription	Primary B cells from cord blood	blood
44	chr7:65991400-66006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr7:65991600-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:65991800-66007600	Weak transcription	NH-A	brain
47	chr7:65992000-65994400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:65992000-66005000	Weak transcription	Left Ventricle	heart
49	chr7:65992200-65993800	Weak transcription	Fetal Lung	lung
50	chr7:65992200-65994600	Weak transcription	Duodenum Mucosa	Duodenum

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