Variant report

Variant	rs17747530
Chromosome Location	chr7:65994729-65994730
allele	C/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
5	lnc-SBDS-4	chr7:65994516-65995124	NONHSAT121202

Extended variants
information (count: 121 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10107	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10265311	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10271548	0.83[ASN][1000 genomes]
rs10274883	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10278014	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10807704	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1083554	0.81[EUR][1000 genomes]
rs10950043	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10950046	0.80[ASN][1000 genomes]
rs11763189	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11765791	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11772884	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11773628	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12333370	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12668005	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12673450	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12698522	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12698526	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13226170	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232191	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13240501	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13242290	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13308803	0.82[EUR][1000 genomes]
rs13536	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860469	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860472	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1968126	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013908	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2024192	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2109295	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109297	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2420599	0.80[AFR][1000 genomes]
rs2420608	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2420610	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420611	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659890	0.82[EUR][1000 genomes]
rs2659891	0.82[EUR][1000 genomes]
rs2659892	0.82[EUR][1000 genomes]
rs2659893	0.82[EUR][1000 genomes]
rs2659896	0.81[EUR][1000 genomes]
rs2659898	0.82[EUR][1000 genomes]
rs2659901	0.82[EUR][1000 genomes]
rs2659907	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659908	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2707824	0.82[EUR][1000 genomes]
rs2707837	0.81[EUR][1000 genomes]
rs2707847	0.82[EUR][1000 genomes]
rs28431318	0.84[ASN][1000 genomes]
rs28480509	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28617601	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28714531	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28731376	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2901209	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2909688	0.81[EUR][1000 genomes]
rs35378740	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3846973	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3857685	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3926380	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4506088	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4717315	0.82[EUR][1000 genomes]
rs4718356	0.81[EUR][1000 genomes]
rs4718358	0.83[AFR][1000 genomes]
rs4718377	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718383	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57739047	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58347342	0.81[EUR][1000 genomes]
rs61348003	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460301	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6460302	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6460303	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460304	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66981195	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6945775	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6951302	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6951946	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6955837	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958200	0.81[AFR][1000 genomes]
rs6963228	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6971059	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6973249	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6976714	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6978028	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6978178	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6980451	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs721717	0.88[ASN][1000 genomes]
rs7384021	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7385102	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7778322	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7782587	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778690	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs778697	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778705	0.82[EUR][1000 genomes]
rs778707	0.82[EUR][1000 genomes]
rs7788984	0.81[AFR][1000 genomes]
rs7789615	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7792762	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7793723	0.90[ASN][1000 genomes]
rs7808013	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801194	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801195	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs801202	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801203	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801204	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs801206	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801208	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs801209	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs801215	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs881285	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9791712	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9791713	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs17747530	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs17747530	RP4-756H11.3	cis	Thyroid	GTEx
rs17747530	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs17747530	LINC00174	cis	Thyroid	GTEx
rs17747530	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs17747530	GTF2IRD1P1	cis	Thyroid	GTEx
rs17747530	GS1-124K5.4	cis	Artery Aorta	GTEx
rs17747530	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs17747530	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs17747530	RP4-756H11.3	cis	lung	GTEx
rs17747530	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs17747530	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs17747530	GS1-124K5.11	cis	Thyroid	GTEx
rs17747530	GS1-124K5.4	cis	Stomach	GTEx
rs17747530	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs17747530	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs17747530	RP4-756H11.3	cis	Artery Tibial	GTEx
rs17747530	GS1-124K5.2	cis	Whole Blood	GTEx
rs17747530	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs17747530	RNU6-96P	cis	Thyroid	GTEx

Chromatin state (count:85 , 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	chr7:65987400-65994800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:65987800-65995000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:65987800-66006200	Weak transcription	Gastric	stomach
9	chr7:65988000-65995000	Weak transcription	Brain Angular Gyrus	brain
10	chr7:65988400-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:65988600-66006200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:65988600-66009000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:65988600-66009000	Weak transcription	HSMMtube	muscle
14	chr7:65988800-65996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:65988800-66008200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr7:65989000-66006200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:65989000-66007600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:65989400-65996800	Strong transcription	Fetal Stomach	stomach
19	chr7:65989400-65998800	Weak transcription	Right Atrium	heart
20	chr7:65989600-65996400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:65989600-65997000	Strong transcription	Fetal Intestine Small	intestine
22	chr7:65989800-65994800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:65989800-65995000	Weak transcription	Placenta	Placenta
24	chr7:65989800-66004200	Weak transcription	Dnd41	blood
25	chr7:65990000-66009000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:65990600-66004000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:65990600-66005600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:65991200-66009800	Weak transcription	Small Intestine	intestine
29	chr7:65991400-66006200	Weak transcription	Primary B cells from cord blood	blood
30	chr7:65991400-66006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:65991600-66006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:65991800-66007600	Weak transcription	NH-A	brain
33	chr7:65992000-66005000	Weak transcription	Left Ventricle	heart
34	chr7:65992200-65996800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:65992400-65994800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:65992400-66006200	Weak transcription	Osteobl	bone
37	chr7:65992600-65996800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:65992600-65996800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr7:65992800-65995600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr7:65992800-65998600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:65992800-66001200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:65993000-65994800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:65993000-65995200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:65993000-65997000	Strong transcription	Lung	lung
45	chr7:65993000-66006200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr7:65993200-65996600	Strong transcription	Adipose Nuclei	Adipose
47	chr7:65993200-65999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:65993400-65995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr7:65993400-65995000	Weak transcription	Esophagus	oesophagus
50	chr7:65993400-65996800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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