Variant report

Variant	rs1527965
Chromosome Location	chr2:62814985-62814986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM17-2	chr2:62814590-62815055	NONHSAT071022
2	lnc-TMEM17-2	chr2:62814590-62815055	NONHSAT071023

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1014119	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183859	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10208675	0.81[CEU][hapmap]
rs1021268	0.88[ASN][1000 genomes]
rs10221574	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12691187	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713463	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713465	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13386935	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13396557	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13422188	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1386399	0.95[YRI][hapmap]
rs1527967	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1534420	0.82[MKK][hapmap];0.95[YRI][hapmap]
rs1601674	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1872788	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1906200	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1906201	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1906202	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2204656	0.95[YRI][hapmap]
rs4271755	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4502392	0.84[EUR][1000 genomes]
rs4671429	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671432	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62180020	0.80[AFR][1000 genomes]
rs6545961	0.80[AFR][1000 genomes]
rs6545962	0.80[AFR][1000 genomes]
rs6753844	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760804	0.80[CEU][hapmap]
rs7603495	0.88[EUR][1000 genomes]
rs901530	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9636442	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9677313	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr2:62798600-62818400	Weak transcription	Esophagus	oesophagus
2	chr2:62813400-62815200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:62813400-62819400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:62813600-62819200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:62813800-62815200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:62814000-62815000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:62814000-62815000	Enhancers	Osteobl	bone
8	chr2:62814000-62815200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:62814000-62815200	Enhancers	NHEK	skin
10	chr2:62814200-62815000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:62814200-62815000	Enhancers	NHLF	lung
12	chr2:62814200-62815200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:62814200-62815200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:62814200-62815200	Enhancers	Brain Angular Gyrus	brain
15	chr2:62814200-62815200	Enhancers	HMEC	breast
16	chr2:62814200-62815200	Enhancers	HSMMtube	muscle
17	chr2:62814200-62815200	Enhancers	NH-A	brain
18	chr2:62814200-62815400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:62814200-62818000	Enhancers	HepG2	liver
20	chr2:62814400-62815000	Enhancers	Brain Hippocampus Middle	brain
21	chr2:62814400-62815200	Enhancers	Brain Anterior Caudate	brain
22	chr2:62814400-62815200	Enhancers	HSMM	muscle
23	chr2:62814600-62815000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:62814600-62815000	Enhancers	GM12878-XiMat	blood
25	chr2:62814600-62818400	Enhancers	Brain Substantia Nigra	brain
26	chr2:62814800-62815000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:62814800-62815200	Enhancers	Fetal Stomach	stomach
28	chr2:62814800-62816200	Weak transcription	NHDF-Ad	bronchial
29	chr2:62814800-62817800	Enhancers	Brain Cingulate Gyrus	brain

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