Variant report

Variant	rs1870708
Chromosome Location	chr3:115975401-115975402
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10934323	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934324	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934326	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11719629	0.90[ASN][1000 genomes]
rs12492442	0.82[JPT][hapmap]
rs12494106	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495309	0.80[ASN][1000 genomes]
rs12496133	0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634800	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695324	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095238	1.00[JPT][hapmap];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	0.82[JPT][hapmap];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	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549832	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824649	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];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]
rs16824691	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs16824693	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16824696	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16845196	0.81[CEU][hapmap]
rs1870707	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870709	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1993732	0.90[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];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	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306064	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];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	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831126	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4831127	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831128	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];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	0.85[CHB][hapmap];0.90[JPT][hapmap];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	0.85[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];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	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7642172	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645796	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	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835427	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9836711	0.82[EUR][1000 genomes]
rs9836892	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850908	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[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	0.85[CHB][hapmap];0.90[JPT][hapmap];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
rs1870708	LSAMP	cis	lung	GTEx

Chromatin state (count:29 , 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	chr3:115971400-115975800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:115971600-115975800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:115971800-115975600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:115972400-115976000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:115972600-115975600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:115972800-115975600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:115972800-115975800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:115973000-115975600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:115973000-115975600	Weak transcription	Brain Substantia Nigra	brain
14	chr3:115973000-115975800	Weak transcription	Brain Angular Gyrus	brain
15	chr3:115973000-115983800	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:115973200-115977000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:115973400-115976200	Enhancers	Fetal Lung	lung
18	chr3:115973600-115975600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:115974400-115975800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:115974600-115975600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:115974800-115975600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:115975000-115976000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:115975000-115976800	Enhancers	Fetal Kidney	kidney
24	chr3:115975200-115976000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:115975200-115978000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:115975400-115975600	Enhancers	NHDF-Ad	bronchial
27	chr3:115975400-115975800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr3:115975400-115976400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:115975400-115976400	Enhancers	Rectal Smooth Muscle	rectum

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