Variant report

Variant	rs4147304
Chromosome Location	chr3:115988415-115988416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10934323	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934324	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934326	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11719629	0.84[ASN][1000 genomes]
rs12494106	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496133	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12634800	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12695324	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13095238	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1381068	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1381070	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1431512	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1461121	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1461125	0.88[ASN][1000 genomes]
rs1461126	0.88[ASN][1000 genomes]
rs1544994	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1549831	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1549832	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824649	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16824686	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16824693	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16824696	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1870707	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1870708	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1870709	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1993732	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163505	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279109	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306064	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2867101	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2867102	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2903483	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3195	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34500521	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4831090	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831126	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4831127	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831128	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61254748	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6438308	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438310	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6765043	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778040	0.88[ASN][1000 genomes]
rs6805045	0.88[ASN][1000 genomes]
rs73141002	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73143006	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73143010	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73861405	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7426468	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7431707	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7624352	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637684	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7642172	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7645796	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7653282	0.88[ASN][1000 genomes]
rs9826213	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9828943	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9830749	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9835427	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9836711	0.80[EUR][1000 genomes]
rs9836892	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850908	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9866532	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866706	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9875017	0.82[EUR][1000 genomes];0.88[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	nsv3957	chr3:115986950-116032625	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4147304	LSAMP	cis	lung	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115984600-115989800	Weak transcription	Brain Substantia Nigra	brain
2	chr3:115985200-115994600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:115985400-115989200	Weak transcription	Fetal Lung	lung
4	chr3:115985400-115989400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:115985400-115992200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:115985400-115999600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:115987000-115989400	Enhancers	Brain Anterior Caudate	brain
8	chr3:115987200-115995400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:115987400-115990200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:115987400-116006200	Weak transcription	Brain Angular Gyrus	brain
11	chr3:115988000-115988600	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr3:115988000-115995600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:115988000-115998200	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:115988200-115996600	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:115988400-115989000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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