Variant report

Variant	rs6460298
Chromosome Location	chr7:65907770-65907771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10261710	0.87[EUR][1000 genomes]
rs1065265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10950035	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10950036	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10950040	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11763224	0.89[EUR][1000 genomes]
rs11766183	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11767262	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11769702	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11770063	0.91[EUR][1000 genomes]
rs12668269	0.85[EUR][1000 genomes]
rs12668859	0.90[ASN][1000 genomes]
rs12670811	0.86[EUR][1000 genomes]
rs12672427	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12672544	0.84[ASN][1000 genomes]
rs1267814	0.81[EUR][1000 genomes]
rs13311962	0.81[EUR][1000 genomes]
rs1547529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1638724	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1638735	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17138149	0.86[EUR][1000 genomes]
rs17138156	0.91[EUR][1000 genomes]
rs1796218	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1796226	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs1796227	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1862085	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1909508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2173571	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2279757	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2420456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2420612	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2707851	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs35459055	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3936065	0.89[EUR][1000 genomes]
rs4718325	0.85[EUR][1000 genomes]
rs4718335	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4718346	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718348	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718364	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6460281	0.86[EUR][1000 genomes]
rs66594357	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67775320	0.80[EUR][1000 genomes]
rs6945896	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6950988	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6960848	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6961853	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6969224	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6970498	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6979636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73142233	0.85[EUR][1000 genomes]
rs73142245	0.87[EUR][1000 genomes]
rs73142265	0.88[EUR][1000 genomes]
rs73146609	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73148639	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73148689	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73150604	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73152714	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7782212	0.85[EUR][1000 genomes]
rs7783889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7785117	0.89[EUR][1000 genomes]
rs7786735	0.85[EUR][1000 genomes]
rs7801332	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7810213	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7811204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801199	0.81[EUR][1000 genomes]
rs801210	0.81[EUR][1000 genomes]
rs801212	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs801213	0.81[EUR][1000 genomes]
rs964971	1.00[CEU][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1802195	chr7:65886451-65945211	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1027068	chr7:65901543-65991211	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv966832	chr7:65901934-65916028	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6460298	GS1-124K5.11	cis	Thyroid	GTEx
rs6460298	GS1-124K5.4	cis	Stomach	GTEx
rs6460298	GTF2IRD1P1	cis	Thyroid	GTEx
rs6460298	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6460298	RNU6-96P	cis	Thyroid	GTEx
rs6460298	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6460298	GS1-124K5.4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
3	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
4	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:65879200-65946000	Weak transcription	NHEK	skin
6	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
7	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
9	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
10	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
13	chr7:65879600-65913600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr7:65879600-65919000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr7:65879600-65920400	Weak transcription	Primary B cells from cord blood	blood
16	chr7:65879800-65913600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:65884000-65919600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr7:65886000-65913600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr7:65886600-65920400	Weak transcription	Right Ventricle	heart
20	chr7:65887000-65924600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr7:65887000-65924600	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:65889200-65939600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr7:65889600-65913800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:65890000-65928800	Weak transcription	Adipose Nuclei	Adipose
25	chr7:65890400-65916200	Weak transcription	Fetal Thymus	thymus
26	chr7:65891600-65939000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:65892000-65931800	Weak transcription	Ovary	ovary
28	chr7:65893200-65913400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:65894200-65939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:65894800-65914000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:65895200-65913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:65897600-65913200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:65898200-65938200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:65900200-65913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:65900200-65913800	Weak transcription	Fetal Stomach	stomach
36	chr7:65900400-65911000	Weak transcription	Fetal Muscle Leg	muscle
37	chr7:65900800-65912200	Weak transcription	Primary T cells from cord blood	blood
38	chr7:65903000-65922000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:65904400-65909600	Weak transcription	Placenta	Placenta
40	chr7:65904400-65939000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr7:65905000-65908600	Weak transcription	HUVEC	blood vessel
42	chr7:65905000-65909000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr7:65905000-65913200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:65905400-65909800	Enhancers	HepG2	liver
45	chr7:65905600-65908000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:65905600-65938600	Weak transcription	Pancreas	Pancrea
47	chr7:65905600-65957600	Weak transcription	Fetal Lung	lung
48	chr7:65905800-65909000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:65906000-65908800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:65906000-65940200	Weak transcription	Fetal Intestine Large	intestine

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