Variant report

Variant	rs4749098
Chromosome Location	chr10:26483710-26483711
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10508711	0.88[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10508712	0.88[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10764599	0.90[ASN][1000 genomes]
rs10828949	0.81[CEU][hapmap]
rs10828950	0.88[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs10828951	0.88[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs10828954	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10828957	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10828958	0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10828961	0.94[ASN][1000 genomes]
rs10828962	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11014917	0.81[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs11014930	0.83[CEU][hapmap]
rs11014953	0.88[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs11014954	0.82[EUR][1000 genomes]
rs11014955	0.88[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs11014960	0.88[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11014983	0.88[CEU][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11599503	0.86[EUR][1000 genomes]
rs12219979	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12269307	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12573019	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs12764197	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773851	0.82[EUR][1000 genomes]
rs12775931	0.82[EUR][1000 genomes]
rs12779517	0.81[EUR][1000 genomes]
rs12781541	0.82[ASW][hapmap];0.88[CEU][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1339811	0.81[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs1361713	0.88[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17752077	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17752353	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1935483	0.82[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1996715	0.81[CEU][hapmap]
rs2000255	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2051084	0.87[ASN][1000 genomes]
rs2275727	0.88[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2887177	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34240977	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34966498	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737316	0.88[CEU][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3781117	0.84[CHB][hapmap]
rs3817416	0.88[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs3818957	0.88[CEU][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4526683	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4747546	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749090	0.90[MEX][hapmap]
rs4749092	0.88[CEU][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4749094	0.87[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6482535	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7083144	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7083433	0.83[ASN][1000 genomes]
rs7905083	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7908081	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7915636	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4749098	SHANK3	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26474000-26491000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr10:26483000-26486600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:26483200-26489000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr10:26483600-26488600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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