Variant report

Variant	rs2306064
Chromosome Location	chr3:115975853-115975854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10934323	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934324	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934326	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11719629	0.90[ASN][1000 genomes]
rs12494106	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495309	0.80[ASN][1000 genomes]
rs12496133	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634800	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695324	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095238	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381068	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381070	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1431512	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1461121	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1461125	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1461126	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1544994	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549831	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549832	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824649	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16824686	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16824693	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16824696	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870707	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870708	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870709	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1993732	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2163505	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279109	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867101	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2867102	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2903483	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3195	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34500521	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4147304	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831090	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831126	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4831127	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831128	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61254748	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6438308	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6438310	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6765043	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6778040	0.94[ASN][1000 genomes]
rs6805045	0.94[ASN][1000 genomes]
rs73141002	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73143006	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73143010	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73861405	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7426468	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431707	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7624352	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637684	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7642172	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645796	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7653282	0.94[ASN][1000 genomes]
rs9826213	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828943	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830749	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835427	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9836711	0.82[EUR][1000 genomes]
rs9836892	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850908	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866532	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9866706	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9875017	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877360	chr3:115916171-116023990	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	esv1808373	chr3:115952799-115984473	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2306064	LSAMP	cis	lung	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115962400-115983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:115965800-115983200	Weak transcription	Fetal Brain Male	brain
3	chr3:115970800-115976800	Enhancers	Colon Smooth Muscle	Colon
4	chr3:115971200-115984800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:115972400-115976000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:115973000-115983800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:115973200-115977000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:115973400-115976200	Enhancers	Fetal Lung	lung
9	chr3:115975000-115976000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:115975000-115976800	Enhancers	Fetal Kidney	kidney
11	chr3:115975200-115976000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:115975200-115978000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:115975400-115976400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:115975400-115976400	Enhancers	Rectal Smooth Muscle	rectum
15	chr3:115975600-115976000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
16	chr3:115975600-115976000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:115975600-115976000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
18	chr3:115975600-115976000	Enhancers	Brain Anterior Caudate	brain
19	chr3:115975600-115976000	Flanking Active TSS	NHDF-Ad	bronchial
20	chr3:115975600-115976200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr3:115975600-115976200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:115975600-115976200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
23	chr3:115975600-115976200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:115975600-115976200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr3:115975600-115976200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:115975600-115976600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr3:115975600-115976600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:115975600-115977000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr3:115975600-115978400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
30	chr3:115975800-115976200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:115975800-115976200	Enhancers	Brain Angular Gyrus	brain
32	chr3:115975800-115976200	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:115975800-115976400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:115975800-115976400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr3:115975800-115976400	Enhancers	NH-A	brain
36	chr3:115975800-115976600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:115975800-115976600	Weak transcription	Brain Substantia Nigra	brain
38	chr3:115975800-115976800	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links