Variant report

Variant	rs1715518
Chromosome Location	chr7:84041488-84041489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM3-4	chr7:84038231-84042095	ucscGeneNc_uc003uia_1

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1228866	0.98[ASN][1000 genomes]
rs1228868	0.98[ASN][1000 genomes]
rs1228946	0.91[ASN][1000 genomes]
rs1228951	0.99[ASN][1000 genomes]
rs1228956	0.99[ASN][1000 genomes]
rs13227369	0.83[ASN][1000 genomes]
rs1520102	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557791	0.83[ASN][1000 genomes]
rs1634605	1.00[ASN][1000 genomes]
rs16887703	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17158998	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17159006	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1922349	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2106965	0.83[ASN][1000 genomes]
rs2214749	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428807	0.99[ASN][1000 genomes]
rs2522370	0.81[AFR][1000 genomes]
rs2527522	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2527527	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2527529	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2527530	0.90[ASN][1000 genomes]
rs2527532	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2527533	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2527535	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2527536	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2527537	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2527538	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2706903	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2706904	0.81[EUR][1000 genomes]
rs2706905	0.81[EUR][1000 genomes]
rs2706912	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2706913	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2706916	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2715032	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2715037	0.89[ASN][1000 genomes]
rs2715044	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2715045	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2715046	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2715047	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2888322	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4016106	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs520178	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526991	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs529539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs530698	0.98[ASN][1000 genomes]
rs531582	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555632	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs559041	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56144625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561955	0.98[ASN][1000 genomes]
rs620373	0.81[EUR][1000 genomes]
rs625480	0.98[ASN][1000 genomes]
rs73711542	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73711549	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783073	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2754468	chr7:83851249-84166749	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1023848	chr7:83985028-84101774	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2761342	chr7:83985028-84101798	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv534431	chr7:84001059-84138511	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv949446	chr7:84003501-84763823	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:84038800-84042800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:84039000-84043000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:84041000-84042600	Enhancers	Hela-S3	cervix
4	chr7:84041000-84042600	Enhancers	HMEC	breast
5	chr7:84041200-84041600	Flanking Active TSS	NH-A	brain
6	chr7:84041200-84041600	Flanking Active TSS	NHLF	lung
7	chr7:84041200-84042000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:84041200-84042000	Flanking Active TSS	NHDF-Ad	bronchial
9	chr7:84041200-84042200	Enhancers	HSMM	muscle
10	chr7:84041200-84042800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:84041200-84043000	Flanking Active TSS	A549	lung
12	chr7:84041400-84041600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:84041400-84041600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:84041400-84041600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:84041400-84041600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr7:84041400-84041600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:84041400-84041600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:84041400-84041600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:84041400-84041600	Flanking Active TSS	NHEK	skin
20	chr7:84041400-84041800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:84041400-84041800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:84041400-84041800	Enhancers	Fetal Intestine Large	intestine
23	chr7:84041400-84041800	Enhancers	Fetal Intestine Small	intestine
24	chr7:84041400-84041800	Flanking Active TSS	Osteobl	bone
25	chr7:84041400-84042000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:84041400-84042000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr7:84041400-84042200	Enhancers	HUVEC	blood vessel
28	chr7:84041400-84042400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:84041400-84043000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links