Variant report

Variant	rs6464824
Chromosome Location	chr7:147257915-147257916
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10223936	0.93[ASN][1000 genomes]
rs10223972	0.93[ASN][1000 genomes]
rs10226013	0.81[CEU][hapmap]
rs10226112	0.88[CEU][hapmap]
rs10226255	0.81[CEU][hapmap]
rs10226376	0.88[CEU][hapmap]
rs10226389	0.88[CEU][hapmap]
rs10226499	0.84[CEU][hapmap]
rs10227024	0.87[CEU][hapmap]
rs10236087	0.88[CEU][hapmap]
rs10237202	0.88[CEU][hapmap]
rs10240182	0.86[CEU][hapmap]
rs10244311	0.83[CEU][hapmap]
rs10244661	0.81[CEU][hapmap]
rs10244825	0.88[CEU][hapmap]
rs10245208	0.88[CEU][hapmap]
rs10248888	0.84[CEU][hapmap]
rs10250480	0.88[CEU][hapmap]
rs10250939	0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10254989	0.81[CEU][hapmap]
rs10255433	0.87[CEU][hapmap]
rs10257834	0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs10259411	0.84[CEU][hapmap]
rs10261388	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10261996	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10264004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10266173	0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10269376	0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10269610	0.93[ASN][1000 genomes]
rs10269768	0.84[CEU][hapmap]
rs10270024	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270032	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272825	0.93[ASN][1000 genomes]
rs10273288	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10273613	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10275373	0.84[CEU][hapmap]
rs10275604	0.84[CEU][hapmap]
rs10279399	0.93[ASN][1000 genomes]
rs10281966	0.88[CEU][hapmap]
rs10952695	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10952703	0.84[CEU][hapmap]
rs1157301	0.91[CEU][hapmap]
rs1157302	0.87[CEU][hapmap]
rs11768141	0.93[ASN][1000 genomes]
rs11773848	0.84[CEU][hapmap]
rs12532801	0.81[CEU][hapmap]
rs12532853	0.81[CEU][hapmap]
rs12534582	0.82[CEU][hapmap]
rs12539891	0.81[CEU][hapmap]
rs12666239	0.88[CEU][hapmap]
rs13232091	0.91[ASN][1000 genomes]
rs1859549	0.93[ASN][1000 genomes]
rs2051875	0.91[CEU][hapmap]
rs2074713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2074714	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs2074715	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs2107858	0.90[CEU][hapmap]
rs2107859	0.83[CEU][hapmap]
rs2107861	0.88[CEU][hapmap]
rs2158640	0.88[CEU][hapmap]
rs2189998	0.88[CEU][hapmap]
rs2189999	0.88[CEU][hapmap]
rs2190000	0.93[ASN][1000 genomes]
rs2190001	0.93[ASN][1000 genomes]
rs2190002	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2190003	0.93[ASN][1000 genomes]
rs2190004	0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2190005	0.93[ASN][1000 genomes]
rs2190006	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190007	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214735	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2240376	0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs2373103	0.88[CEU][hapmap]
rs2373104	0.90[CEU][hapmap]
rs41354149	0.84[CEU][hapmap]
rs4615480	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs5003024	0.88[CEU][hapmap]
rs6464821	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6464823	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6464830	0.84[CEU][hapmap]
rs6944540	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6944808	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6946882	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6952758	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs6954225	0.84[CEU][hapmap]
rs6957033	0.80[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs6959784	0.84[CEU][hapmap]
rs6962824	0.90[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6962950	0.93[ASN][1000 genomes]
rs6963584	0.88[CEU][hapmap]
rs6966095	0.93[ASN][1000 genomes]
rs6967426	0.81[CEU][hapmap]
rs6967780	0.81[CEU][hapmap]
rs6967857	0.84[CEU][hapmap]
rs6973502	0.90[CEU][hapmap]
rs6975276	0.86[CEU][hapmap]
rs6975841	0.82[JPT][hapmap]
rs6978578	0.91[ASN][1000 genomes]
rs6979099	0.92[CEU][hapmap]
rs6980002	0.90[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6980460	0.90[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7459220	0.88[CEU][hapmap]
rs7783132	0.83[CEU][hapmap]
rs7796991	0.81[CEU][hapmap]
rs7799324	0.86[CEU][hapmap]
rs7802526	0.87[CEU][hapmap]
rs7805454	0.88[CEU][hapmap]
rs7805615	0.86[CEU][hapmap]
rs851816	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs851817	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs851821	0.82[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs851823	0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs851824	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs851826	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs851828	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs929353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985829	0.88[CEU][hapmap]
rs988041	0.81[CEU][hapmap]
rs988042	0.81[CEU][hapmap]
rs989241	0.88[CEU][hapmap]
rs989242	0.87[CEU][hapmap]
rs989243	0.88[CEU][hapmap]
rs995890	0.91[CEU][hapmap]
rs995891	0.95[CEU][hapmap]
rs995892	0.87[CEU][hapmap]
rs995893	0.87[CEU][hapmap]

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	nsv931005	chr7:146730472-147381257	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6464824	CNTNAP2	cis	cerebellum	SCAN
rs6464824	CUL1	cis	parietal	SCAN
rs6464824	ABCB8	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147257600-147258000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:147257600-147258000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:147257800-147258400	Enhancers	HUES48 Cell Line	embryonic stem cell

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