Variant report

Variant	rs72950898
Chromosome Location	chr1:85618999-85619000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYDE2-1	chr1:85618178-85619886	NONHSAT004237

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11161536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11161537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11161544	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11161546	1.00[AMR][1000 genomes]
rs12073567	0.85[AMR][1000 genomes]
rs12075407	1.00[AMR][1000 genomes]
rs12083953	1.00[AMR][1000 genomes]
rs12087427	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12096033	0.80[AFR][1000 genomes]
rs58859506	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72482805	0.88[AFR][1000 genomes]
rs72950882	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950887	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952616	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952618	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952624	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952634	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7513769	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85603800-85632200	Weak transcription	Fetal Lung	lung
2	chr1:85608600-85655200	Weak transcription	Aorta	Aorta
3	chr1:85608800-85629200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:85610400-85647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:85610600-85630600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:85611400-85629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:85614800-85619000	Weak transcription	Right Atrium	heart
8	chr1:85615000-85621800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:85615400-85647600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:85615400-85655200	Weak transcription	Lung	lung
11	chr1:85615600-85654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:85615800-85625200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:85615800-85627200	Weak transcription	Ovary	ovary
14	chr1:85615800-85627600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:85615800-85629400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:85615800-85630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:85615800-85632800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:85615800-85665800	Weak transcription	Esophagus	oesophagus
19	chr1:85616000-85632200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:85616000-85634600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:85616000-85638800	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:85616400-85627600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:85616400-85635800	Weak transcription	Left Ventricle	heart
24	chr1:85617000-85619400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:85617400-85619200	Weak transcription	Fetal Intestine Large	intestine
26	chr1:85617600-85619000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:85617600-85619000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:85617800-85648000	Weak transcription	Liver	Liver
29	chr1:85618400-85619000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:85618600-85619000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:85618600-85619800	Enhancers	Fetal Heart	heart
32	chr1:85618800-85619000	Enhancers	Gastric	stomach
33	chr1:85618800-85619200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:85618800-85619400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:85618800-85619800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:85618800-85619800	Flanking Active TSS	GM12878-XiMat	blood

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