Variant report

Variant	rs2840274
Chromosome Location	chr1:184210805-184210806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10047173	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1006198	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10442605	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10797946	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797947	0.89[ASN][1000 genomes]
rs10911524	0.83[ASN][1000 genomes]
rs10911526	0.83[ASN][1000 genomes]
rs10911527	0.83[ASN][1000 genomes]
rs10911530	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911531	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911532	0.86[ASN][1000 genomes]
rs10911555	0.95[CHB][hapmap]
rs1111088	0.81[EUR][1000 genomes]
rs11585071	0.86[CHB][hapmap]
rs11806061	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12120085	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12128572	0.83[ASN][1000 genomes]
rs12136077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139463	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12139516	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139721	0.80[EUR][1000 genomes]
rs1327139	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1327147	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359760	0.83[ASN][1000 genomes]
rs1409809	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1571972	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1831055	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1831056	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1854086	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863155	0.83[ASN][1000 genomes]
rs1863156	0.83[ASN][1000 genomes]
rs1863157	0.83[ASN][1000 genomes]
rs1889025	0.90[ASN][1000 genomes]
rs1889026	0.90[ASN][1000 genomes]
rs2019376	0.86[ASN][1000 genomes]
rs2081401	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2081402	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2081403	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2151172	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2161988	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2194698	0.83[ASN][1000 genomes]
rs2216932	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2378824	0.93[ASN][1000 genomes]
rs2378825	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2378841	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3954285	0.83[ASN][1000 genomes]
rs4292918	0.91[ASN][1000 genomes]
rs4342818	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4428848	0.95[CHB][hapmap]
rs4650663	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4650664	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4651182	0.83[ASN][1000 genomes]
rs4651186	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651189	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651190	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651191	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4651192	0.82[ASN][1000 genomes]
rs4651193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651195	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4651197	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4651200	0.95[CHB][hapmap]
rs4990766	0.87[ASN][1000 genomes]
rs56308906	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6424933	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6424934	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6424937	0.84[ASN][1000 genomes]
rs6424939	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6424940	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6424944	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6667352	0.86[ASN][1000 genomes]
rs6676366	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678460	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689088	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695243	0.81[EUR][1000 genomes]
rs6702498	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs714625	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522326	0.81[EUR][1000 genomes]
rs7530243	0.86[CHB][hapmap]
rs7549600	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551423	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs929941	0.83[ASN][1000 genomes]
rs932993	0.91[CHB][hapmap]
rs963234	0.95[CHB][hapmap]
rs9787399	0.95[CHB][hapmap]
rs9803635	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9803849	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9803931	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9804048	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs993065	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2840274	RALGPS2	cis	parietal	SCAN
rs2840274	NMNAT2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184207000-184211800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:184210200-184212000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:184210600-184211400	Weak transcription	Left Ventricle	heart
4	chr1:184210800-184212400	Enhancers	Small Intestine	intestine

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