Variant report

Variant	rs4146411
Chromosome Location	chr4:97266060-97266061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10002816	0.85[ASN][1000 genomes]
rs10006557	0.85[ASN][1000 genomes]
rs10007900	0.88[ASN][1000 genomes]
rs10015613	0.85[ASN][1000 genomes]
rs10016180	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10021889	0.89[ASN][1000 genomes]
rs10213429	0.88[ASN][1000 genomes]
rs11097501	0.80[ASN][1000 genomes]
rs11097502	0.88[ASN][1000 genomes]
rs11097505	0.91[ASN][1000 genomes]
rs11932384	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11935830	0.84[ASN][1000 genomes]
rs12501360	0.83[ASN][1000 genomes]
rs12508802	0.85[ASN][1000 genomes]
rs12509883	0.87[ASN][1000 genomes]
rs12642471	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12644982	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12650441	0.83[ASN][1000 genomes]
rs13104802	0.90[ASN][1000 genomes]
rs13121458	0.80[ASN][1000 genomes]
rs13122821	0.80[ASN][1000 genomes]
rs13122856	0.81[ASN][1000 genomes]
rs13150508	0.91[ASN][1000 genomes]
rs1354704	0.89[ASN][1000 genomes]
rs1354706	0.89[ASN][1000 genomes]
rs1395199	0.83[ASN][1000 genomes]
rs1444021	0.80[ASN][1000 genomes]
rs1506304	0.91[ASN][1000 genomes]
rs1506305	0.89[ASN][1000 genomes]
rs1506306	0.91[ASN][1000 genomes]
rs1506317	0.82[ASN][1000 genomes]
rs1506318	0.85[ASN][1000 genomes]
rs1506319	0.91[ASN][1000 genomes]
rs1506320	0.85[ASN][1000 genomes]
rs1516676	0.81[ASN][1000 genomes]
rs1567036	0.84[ASN][1000 genomes]
rs1605227	0.92[ASN][1000 genomes]
rs17025209	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs17025493	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1847963	0.83[ASN][1000 genomes]
rs1847964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847966	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1847967	0.85[ASN][1000 genomes]
rs1847968	0.80[ASN][1000 genomes]
rs1847969	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1857889	0.83[ASN][1000 genomes]
rs1867400	0.80[ASN][1000 genomes]
rs1911074	0.85[ASN][1000 genomes]
rs1911076	0.91[ASN][1000 genomes]
rs1911077	0.90[ASN][1000 genomes]
rs1948912	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048022	0.88[ASN][1000 genomes]
rs2083922	0.85[ASN][1000 genomes]
rs2113973	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2174584	0.89[ASN][1000 genomes]
rs2197322	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs28407945	0.91[ASN][1000 genomes]
rs28523416	0.91[ASN][1000 genomes]
rs28565871	0.91[ASN][1000 genomes]
rs28633781	0.83[ASN][1000 genomes]
rs2865736	0.85[ASN][1000 genomes]
rs28788633	0.88[ASN][1000 genomes]
rs34198564	0.89[ASN][1000 genomes]
rs35257138	0.88[ASN][1000 genomes]
rs36039803	0.85[ASN][1000 genomes]
rs4146410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4293790	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4343731	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4414959	0.83[ASN][1000 genomes]
rs4611939	0.85[ASN][1000 genomes]
rs4613576	0.85[ASN][1000 genomes]
rs4619895	0.91[ASN][1000 genomes]
rs4699283	0.85[ASN][1000 genomes]
rs4699285	0.88[ASN][1000 genomes]
rs4699287	0.90[ASN][1000 genomes]
rs4699288	0.85[ASN][1000 genomes]
rs4699496	0.85[ASN][1000 genomes]
rs4699501	0.85[ASN][1000 genomes]
rs4699503	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699512	0.85[ASN][1000 genomes]
rs4699513	0.85[ASN][1000 genomes]
rs5017329	0.85[ASN][1000 genomes]
rs55680326	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55847611	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58334182	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60275360	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532600	0.87[ASN][1000 genomes]
rs6815558	0.87[ASN][1000 genomes]
rs6815743	0.82[ASN][1000 genomes]
rs6816447	0.91[ASN][1000 genomes]
rs6820075	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830120	0.89[ASN][1000 genomes]
rs6832934	0.91[ASN][1000 genomes]
rs6835808	0.84[ASN][1000 genomes]
rs6837318	0.87[ASN][1000 genomes]
rs6841294	0.85[ASN][1000 genomes]
rs6855768	0.84[ASN][1000 genomes]
rs6857113	0.87[ASN][1000 genomes]
rs72880179	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72880182	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72883800	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72885446	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72885485	0.91[ASN][1000 genomes]
rs7653937	0.83[ASN][1000 genomes]
rs766061	0.83[ASN][1000 genomes]
rs7671604	0.83[ASN][1000 genomes]
rs7673756	0.89[ASN][1000 genomes]
rs7686174	0.89[ASN][1000 genomes]
rs7690397	0.85[ASN][1000 genomes]
rs7698381	0.89[ASN][1000 genomes]
rs9307167	0.87[ASN][1000 genomes]
rs9307168	0.88[ASN][1000 genomes]
rs931841	0.91[ASN][1000 genomes]
rs931842	0.91[ASN][1000 genomes]
rs9884259	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9884940	0.88[ASN][1000 genomes]
rs9998383	0.91[ASN][1000 genomes]
rs9999006	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470057	chr4:97104880-97311657	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv461589	chr4:97104881-97311657	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv594916	chr4:97104881-97311657	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv879632	chr4:97118539-97308914	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv461590	chr4:97197036-97266060	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv594917	chr4:97197036-97266060	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4146411	C4orf17	cis	parietal	SCAN
rs4146411	METAP1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:97262800-97270400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:97263400-97266200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:97264000-97268000	Weak transcription	HUVEC	blood vessel
4	chr4:97265000-97266200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:97265000-97266200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:97265200-97266200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:97265200-97273200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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