Variant report

Variant	rs16824691
Chromosome Location	chr3:115982772-115982773
allele	A/T
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];0.91[ASN][1000 genomes]
rs10934324	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10934326	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11719629	0.87[ASN][1000 genomes]
rs11920943	0.82[CHB][hapmap]
rs12492442	0.81[CHB][hapmap]
rs12494106	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496133	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12695324	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13095238	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1381068	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1381070	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1431512	0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1461121	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1461125	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1461126	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1544994	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1549831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549832	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16824649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16824686	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16824693	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16824696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16845196	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs1870707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1870708	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1870709	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1993732	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2163505	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306064	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867101	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867102	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2903483	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34500521	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147304	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4831090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4831126	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831127	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4831128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61254748	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6438308	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438310	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6765043	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6778040	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs6805045	0.91[ASN][1000 genomes]
rs73141002	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73143006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143010	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73861405	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7426468	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7431707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7624352	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7637684	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7642172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7645796	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653282	0.91[ASN][1000 genomes]
rs9826213	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9828943	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9830749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836711	0.81[EUR][1000 genomes]
rs9836892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866532	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9866706	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9875017	0.83[EUR][1000 genomes];0.91[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
rs16824691	LSAMP	cis	lung	GTEx

Chromatin state (count:17 , 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	chr3:115971200-115984800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:115973000-115983800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:115976000-115987000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:115976200-115982800	Weak transcription	Fetal Lung	lung
7	chr3:115976200-115984000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:115976200-115987000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:115978400-115983800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:115979800-115985000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:115980400-115983400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:115982000-115983000	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:115982000-115987200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:115982600-115983200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:115982600-115983400	Enhancers	Rectal Smooth Muscle	rectum
16	chr3:115982600-115983800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:115982600-115985600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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