Variant report

Variant	rs13224319
Chromosome Location	chr7:66007363-66007364
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	chr7:66006231-66007536	ENSG00000249705
2	lnc-SBDS-4	chr7:66006229-66007536	ENSG00000229180
3	lnc-SBDS-4	chr7:66006229-66007536	NONHSAT121200
4	lnc-SBDS-4	chr7:66006229-66007536	ENSG00000229180.4

Extended variants
information (count: 115 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10215132	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10229345	0.90[EUR][1000 genomes]
rs10234018	0.81[ASN][1000 genomes]
rs10249404	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10255377	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10263935	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272357	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10272546	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10274773	0.87[ASN][1000 genomes]
rs10278371	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10278816	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10281080	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10950041	0.83[AFR][1000 genomes]
rs10950044	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11765356	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772264	0.83[ASN][1000 genomes]
rs11773829	0.81[ASN][1000 genomes]
rs12532998	0.82[AFR][1000 genomes]
rs12533585	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12533997	0.81[AFR][1000 genomes]
rs12535036	0.82[AFR][1000 genomes]
rs12698523	0.82[AFR][1000 genomes]
rs12698532	0.86[AFR][1000 genomes]
rs12698534	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13309022	0.81[AFR][1000 genomes]
rs1860468	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1860470	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1961155	0.86[ASN][1000 genomes]
rs1968127	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003301	0.81[ASN][1000 genomes]
rs2013222	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2191268	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2277911	0.82[AFR][1000 genomes]
rs2286683	0.87[ASN][1000 genomes]
rs2286684	0.87[ASN][1000 genomes]
rs2302918	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420824	0.87[ASN][1000 genomes]
rs2420827	0.83[ASN][1000 genomes]
rs2659906	0.83[ASN][1000 genomes]
rs2659909	0.83[ASN][1000 genomes]
rs2659912	0.82[ASN][1000 genomes]
rs2659916	0.82[ASN][1000 genomes]
rs2707827	0.80[ASN][1000 genomes]
rs2707836	0.83[ASN][1000 genomes]
rs2707841	0.83[ASN][1000 genomes]
rs2707849	0.83[ASN][1000 genomes]
rs28698552	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28830215	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35410151	0.80[AFR][1000 genomes]
rs35526611	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35986979	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3735148	0.81[AFR][1000 genomes]
rs3764903	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800823	0.81[ASN][1000 genomes]
rs3857686	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3857688	0.87[ASN][1000 genomes]
rs3898855	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4717310	0.83[ASN][1000 genomes]
rs4718357	0.82[AFR][1000 genomes]
rs4718361	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4718363	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56229325	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62465434	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467857	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460300	0.82[AFR][1000 genomes]
rs6460305	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460308	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460309	0.87[ASN][1000 genomes]
rs6943696	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6947808	0.80[AFR][1000 genomes]
rs6949912	0.85[ASN][1000 genomes]
rs6957199	0.87[AFR][1000 genomes]
rs6958271	0.87[AFR][1000 genomes]
rs6958277	0.86[AFR][1000 genomes]
rs6958520	0.83[ASN][1000 genomes]
rs6960778	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6961186	0.80[AFR][1000 genomes]
rs6965056	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6970030	0.80[AFR][1000 genomes]
rs6970357	0.82[AFR][1000 genomes]
rs6970860	0.87[AFR][1000 genomes]
rs6978429	0.80[AFR][1000 genomes]
rs71563125	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs732465	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7357230	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7779971	0.82[ASN][1000 genomes]
rs7785213	0.87[ASN][1000 genomes]
rs7788576	0.83[ASN][1000 genomes]
rs7789419	0.81[ASN][1000 genomes]
rs7793569	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7807930	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7807944	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801190	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801191	0.80[AFR][1000 genomes]
rs801193	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801196	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801201	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801205	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs801207	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs801211	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801216	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801217	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs810400	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9791890	0.81[EUR][1000 genomes];0.87[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13224319	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs13224319	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs13224319	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs13224319	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs13224319	RP4-756H11.3	cis	Artery Tibial	GTEx
rs13224319	RP4-756H11.3	cis	lung	GTEx
rs13224319	RP4-756H11.3	cis	Artery Aorta	GTEx
rs13224319	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs13224319	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs13224319	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs13224319	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13224319	RP4-756H11.3	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65988600-66009000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:65988600-66009000	Weak transcription	HSMMtube	muscle
3	chr7:65988800-66008200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr7:65989000-66007600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:65990000-66009000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:65991200-66009800	Weak transcription	Small Intestine	intestine
7	chr7:65991800-66007600	Weak transcription	NH-A	brain
8	chr7:65993600-66009000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr7:65993600-66009400	Weak transcription	HSMM	muscle
10	chr7:65994000-66008400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr7:65994000-66014400	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:65995000-66010000	Weak transcription	Fetal Lung	lung
13	chr7:65995000-66017200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:65995200-66009000	Weak transcription	Fetal Thymus	thymus
15	chr7:65995400-66009000	Weak transcription	Brain Angular Gyrus	brain
16	chr7:65995600-66007800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:65999800-66007800	Weak transcription	NHDF-Ad	bronchial
18	chr7:65999800-66022400	Strong transcription	Fetal Stomach	stomach
19	chr7:66000600-66009000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:66000600-66019200	Weak transcription	Fetal Kidney	kidney
21	chr7:66000800-66016600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:66001200-66014400	Weak transcription	A549	lung
23	chr7:66001400-66007400	Weak transcription	Ovary	ovary
24	chr7:66001400-66022400	Weak transcription	Stomach Mucosa	stomach
25	chr7:66002000-66007800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:66002800-66016000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:66003200-66007800	Weak transcription	Hela-S3	cervix
28	chr7:66003400-66007400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:66003600-66018800	Weak transcription	GM12878-XiMat	blood
30	chr7:66003800-66022200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr7:66003800-66022800	Strong transcription	Fetal Intestine Small	intestine
32	chr7:66004200-66007600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:66004200-66010000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:66004200-66012400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:66004400-66007800	Weak transcription	Right Atrium	heart
36	chr7:66004400-66010400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:66004400-66011000	Strong transcription	Spleen	Spleen
38	chr7:66004400-66052600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr7:66004600-66009000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr7:66004600-66009000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:66004600-66016600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr7:66004800-66015400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:66004800-66019200	Weak transcription	HUVEC	blood vessel
44	chr7:66004800-66037200	Weak transcription	Psoas Muscle	Psoas
45	chr7:66005000-66010000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr7:66005000-66014400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr7:66005000-66016800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr7:66005200-66007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr7:66005200-66008000	Weak transcription	Brain Substantia Nigra	brain
50	chr7:66005200-66016600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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