Variant report

Variant	rs73152708
Chromosome Location	chr7:65996437-65996438
allele	C/T
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: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10081172	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10228381	0.81[EUR][1000 genomes]
rs10236665	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10237244	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10247852	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10252133	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10257393	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10262184	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10264619	0.88[EUR][1000 genomes]
rs10267834	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10273320	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10275413	0.89[EUR][1000 genomes]
rs10278343	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10278763	0.81[EUR][1000 genomes]
rs10280431	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10281734	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10479728	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12234826	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12334214	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13437901	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16868546	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17138208	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1862086	0.82[EUR][1000 genomes]
rs1895134	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2420598	0.86[EUR][1000 genomes]
rs28368585	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28455065	0.87[EUR][1000 genomes]
rs28526115	0.81[EUR][1000 genomes]
rs28606020	0.89[EUR][1000 genomes]
rs28615327	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28657758	0.81[EUR][1000 genomes]
rs3757419	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4518552	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4587218	0.86[EUR][1000 genomes]
rs58123804	0.88[EUR][1000 genomes]
rs58973756	0.86[EUR][1000 genomes]
rs60344524	0.82[EUR][1000 genomes]
rs61093354	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6949083	0.86[EUR][1000 genomes]
rs6974601	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73133851	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148698	0.83[EUR][1000 genomes]
rs73152719	0.86[EUR][1000 genomes]
rs73152725	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs73152708	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs73152708	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs73152708	GS1-124K5.12	cis	Artery Tibial	GTEx

Chromatin state (count:90 , 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	chr7:65983600-66000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:65985800-66006200	Weak transcription	Pancreas	Pancrea
6	chr7:65987800-66006200	Weak transcription	Gastric	stomach
7	chr7:65988400-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:65988600-66006200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:65988600-66009000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:65988600-66009000	Weak transcription	HSMMtube	muscle
11	chr7:65988800-66008200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:65989000-66006200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:65989000-66007600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:65989400-65996800	Strong transcription	Fetal Stomach	stomach
15	chr7:65989400-65998800	Weak transcription	Right Atrium	heart
16	chr7:65989600-65997000	Strong transcription	Fetal Intestine Small	intestine
17	chr7:65989800-66004200	Weak transcription	Dnd41	blood
18	chr7:65990000-66009000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:65990600-66004000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:65990600-66005600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:65991200-66009800	Weak transcription	Small Intestine	intestine
22	chr7:65991400-66006200	Weak transcription	Primary B cells from cord blood	blood
23	chr7:65991400-66006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:65991600-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:65991800-66007600	Weak transcription	NH-A	brain
26	chr7:65992000-66005000	Weak transcription	Left Ventricle	heart
27	chr7:65992200-65996800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:65992400-66006200	Weak transcription	Osteobl	bone
29	chr7:65992600-65996800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:65992600-65996800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr7:65992800-65998600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:65992800-66001200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:65993000-65997000	Strong transcription	Lung	lung
34	chr7:65993000-66006200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:65993200-65996600	Strong transcription	Adipose Nuclei	Adipose
36	chr7:65993200-65999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:65993400-65996800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:65993400-66006200	Weak transcription	Colonic Mucosa	Colon
39	chr7:65993600-66006200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:65993600-66009000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:65993600-66009400	Weak transcription	HSMM	muscle
42	chr7:65993800-66006200	Weak transcription	NHEK	skin
43	chr7:65994000-66006200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr7:65994000-66008400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr7:65994000-66014400	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:65994400-65996800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:65994400-65998400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:65994600-65996600	Strong transcription	Spleen	Spleen
49	chr7:65994800-65996600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:65995000-65996800	Strong transcription	Placenta	Placenta

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