Variant report

Variant	rs11014983
Chromosome Location	chr10:26462557-26462558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10508711	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10508712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10764599	0.92[ASN][1000 genomes]
rs10828939	0.86[EUR][1000 genomes]
rs10828941	0.86[EUR][1000 genomes]
rs10828944	0.87[EUR][1000 genomes]
rs10828949	0.94[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs10828950	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10828951	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10828954	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10828957	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10828958	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10828961	0.95[ASN][1000 genomes]
rs10828962	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs11014917	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11014919	0.92[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs11014930	0.92[CEU][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs11014953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11014954	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11014955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11014960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11527599	0.88[EUR][1000 genomes]
rs11599503	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12219979	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12269307	0.94[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12571378	0.86[EUR][1000 genomes]
rs12573019	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12764197	0.82[CEU][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12773851	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12774203	0.88[EUR][1000 genomes]
rs12775931	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12779517	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12781541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1339811	0.94[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1339819	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs1361713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17752077	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17752353	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1935483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1996715	0.94[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2000255	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2051084	0.89[ASN][1000 genomes]
rs2176938	0.86[EUR][1000 genomes]
rs2275727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28796333	0.80[EUR][1000 genomes]
rs2887177	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34240977	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34966498	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3737316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781117	1.00[ASW][hapmap]
rs3817416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3818957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3824706	0.88[EUR][1000 genomes]
rs4526683	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4747546	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4749090	0.82[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs4749092	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4749094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4749098	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]
rs6482535	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7083144	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7083433	0.92[ASN][1000 genomes]
rs7905083	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs7908081	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7915636	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.92[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
rs11014983	SHANK3	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26440800-26473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr10:26453800-26466800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:26459400-26466800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:26460800-26462800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:26461000-26464600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:26461400-26466800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:26461600-26464200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr10:26461800-26464400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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