Variant report

Variant	rs11688226
Chromosome Location	chr2:210770527-210770528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10166289	0.94[EUR][1000 genomes]
rs10189597	0.96[EUR][1000 genomes]
rs10194322	1.00[CEU][hapmap]
rs10194333	1.00[CEU][hapmap]
rs10490025	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10490026	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10490027	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10490028	1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1160565	0.93[EUR][1000 genomes]
rs11682914	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs11691952	0.93[EUR][1000 genomes]
rs11694132	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11695433	0.93[EUR][1000 genomes]
rs12328328	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12328346	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12328866	0.96[EUR][1000 genomes]
rs12328869	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12328884	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12328886	0.96[EUR][1000 genomes]
rs12329111	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12329134	0.96[EUR][1000 genomes]
rs12329303	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12694190	0.93[EUR][1000 genomes]
rs12993178	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13007357	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13010861	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13010864	0.93[EUR][1000 genomes]
rs13013030	1.00[CEU][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13398209	0.96[EUR][1000 genomes]
rs13398411	0.96[EUR][1000 genomes]
rs13414802	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1558474	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs16843821	0.92[EUR][1000 genomes]
rs16843880	0.97[EUR][1000 genomes]
rs16843893	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17748674	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17748692	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17748818	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2109970	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2159746	0.93[EUR][1000 genomes]
rs2159747	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2191908	0.93[EUR][1000 genomes]
rs2191909	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs34038887	0.96[EUR][1000 genomes]
rs34073663	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34115158	0.93[EUR][1000 genomes]
rs34395024	0.93[EUR][1000 genomes]
rs34434902	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34529676	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34920752	0.93[EUR][1000 genomes]
rs35280979	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35365084	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35817243	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35969300	0.93[EUR][1000 genomes]
rs36006352	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6435545	0.84[GIH][hapmap]
rs6712943	0.93[EUR][1000 genomes]
rs6729513	0.93[EUR][1000 genomes]
rs6739769	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6757148	0.93[EUR][1000 genomes]
rs71420778	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7566741	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7567142	0.96[EUR][1000 genomes]
rs7567267	0.96[EUR][1000 genomes]
rs7579121	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7581628	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7581974	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7583147	0.96[EUR][1000 genomes]
rs7584039	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7593426	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7594368	0.93[EUR][1000 genomes]
rs7595063	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7598071	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9630977	0.96[EUR][1000 genomes]
rs9631001	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9677274	0.96[EUR][1000 genomes]
rs9677282	0.96[EUR][1000 genomes]
rs9973317	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9973465	0.94[EUR][1000 genomes]
rs9973473	0.96[EUR][1000 genomes]
rs9973633	0.96[EUR][1000 genomes]
rs9973787	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9973848	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431969	chr2:210682494-211074494	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1004426	chr2:210709999-211001680	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv998029	chr2:210751692-210838759	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1795338	chr2:210758078-211098113	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11688226	IKZF2	cis	cerebellum	SCAN
rs11688226	CREB1	cis	parietal	SCAN
rs11688226	ZDBF2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210733200-210791400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:210737800-210772400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:210742600-210798000	Weak transcription	Brain Germinal Matrix	brain
4	chr2:210745600-210789000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:210769400-210770600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:210769400-210770800	Strong transcription	Brain Anterior Caudate	brain
7	chr2:210769400-210770800	Strong transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:210769600-210770600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:210769600-210778600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:210769800-210772200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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