Variant report

Variant	rs2279109
Chromosome Location	chr3:115974374-115974375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10934323	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934326	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11719629	0.93[ASN][1000 genomes]
rs11920943	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs12492442	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12494106	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496133	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12695324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381068	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381070	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1431512	0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1461121	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1461125	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1461126	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1544994	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1549831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1549832	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16824649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16824686	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16824691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs16824693	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16845196	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap]
rs1870707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1870708	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]
rs1870709	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1993732	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2163505	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306064	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];0.96[ASN][1000 genomes]
rs2867102	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2903483	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34500521	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147304	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4831090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4831126	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4831128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4831129	0.80[CHD][hapmap]
rs61254748	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6438308	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438310	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6765043	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs6805045	0.97[ASN][1000 genomes]
rs73141002	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73143006	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73143010	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73861405	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7426468	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624352	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637684	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7642172	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645796	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653282	0.97[ASN][1000 genomes]
rs9289048	0.81[ASN][1000 genomes]
rs9826213	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9828943	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830749	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9836711	0.81[EUR][1000 genomes]
rs9836892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9866532	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866706	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9874470	0.86[CHD][hapmap]
rs9875017	0.83[EUR][1000 genomes];0.97[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
rs2279109	LSAMP	cis	lung	GTEx

Chromatin state (count:26 , 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	chr3:115970800-115974800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:115970800-115976800	Enhancers	Colon Smooth Muscle	Colon
5	chr3:115971200-115975000	Weak transcription	Fetal Kidney	kidney
6	chr3:115971200-115984800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:115971400-115975800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:115971600-115975800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:115971800-115975600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:115972400-115976000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:115972600-115974400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:115972600-115975400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:115972600-115975600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:115972800-115974400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:115972800-115975600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:115972800-115975800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:115973000-115975600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:115973000-115975600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:115973000-115975800	Weak transcription	Brain Angular Gyrus	brain
20	chr3:115973000-115983800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:115973200-115974400	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:115973200-115977000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:115973400-115976200	Enhancers	Fetal Lung	lung
24	chr3:115973600-115975600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:115973800-115974400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:115974200-115974600	Enhancers	Fetal Stomach	stomach

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