Variant report

Variant	rs10769288
Chromosome Location	chr11:47729180-47729181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1017730	0.94[JPT][hapmap]
rs1056387	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs10742814	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs10742817	0.85[CEU][hapmap];0.94[CHB][hapmap];0.87[TSI][hapmap]
rs10742820	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs10742824	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10769299	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10769300	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs10838732	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10838740	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[TSI][hapmap]
rs10838746	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[TSI][hapmap]
rs10838758	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10838759	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10838760	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs10838771	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10838773	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10838774	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs10838777	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs11039266	0.87[JPT][hapmap]
rs11039280	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs11039329	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[TSI][hapmap]
rs11039345	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs11039373	0.88[CEU][hapmap];0.89[CHB][hapmap]
rs11039377	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap]
rs11039402	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs11039419	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap]
rs12226431	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs12286721	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs12785949	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs1563820	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs1563821	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs17727140	1.00[YRI][hapmap]
rs2170815	0.87[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.87[TSI][hapmap]
rs2203712	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs2280231	0.87[JPT][hapmap]
rs2290851	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs3758655	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs3816605	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap]
rs3886262	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs4539273	0.81[CEU][hapmap];0.94[CHB][hapmap]
rs4752796	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs4752860	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs4752865	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs6485763	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs6485773	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs6485775	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs6485786	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs7108479	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs7110300	0.87[ASW][hapmap];0.84[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs7114813	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs7118178	0.87[JPT][hapmap]
rs7129797	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs754434	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs7929014	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs7932703	0.87[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs7936948	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[TSI][hapmap]
rs7939420	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs7950674	0.87[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10769288	CRY2	cis	parietal	SCAN
rs10769288	MTCH2	cis	cerebellum	SCAN
rs10769288	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10769288	MADD	cis	cerebellum	SCAN
rs10769288	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47705600-47735600	Weak transcription	Primary B cells from cord blood	blood
2	chr11:47712000-47736000	Weak transcription	Fetal Intestine Small	intestine
3	chr11:47722400-47735800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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