Variant report

Variant	rs10490028
Chromosome Location	chr2:210735160-210735161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10166289	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10178431	0.81[ASW][hapmap]
rs10189597	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10194322	0.93[ASW][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs10490025	0.93[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10490026	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10490027	0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1160565	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11682914	0.97[GIH][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11688226	1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11691952	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11694132	0.96[EUR][1000 genomes]
rs11695433	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12328328	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12328346	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12328866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12328869	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12328884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12328886	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12329111	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12329134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12329303	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12694190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12993178	0.97[EUR][1000 genomes]
rs13007357	0.89[EUR][1000 genomes]
rs13010861	0.97[EUR][1000 genomes]
rs13010864	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13013030	0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs13398209	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13398411	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13414802	0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1558474	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16843821	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16843880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16843887	0.92[YRI][hapmap]
rs16843893	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17748674	0.97[EUR][1000 genomes]
rs17748692	0.97[EUR][1000 genomes]
rs17748818	1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2109970	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2159746	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2159747	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2191908	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2191909	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34038887	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34073663	0.97[EUR][1000 genomes]
rs34115158	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34395024	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34434902	0.97[EUR][1000 genomes]
rs34529676	0.96[EUR][1000 genomes]
rs34920752	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35280979	0.96[EUR][1000 genomes]
rs35365084	0.96[EUR][1000 genomes]
rs35817243	0.96[EUR][1000 genomes]
rs35969300	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36006352	0.96[EUR][1000 genomes]
rs6435545	0.84[GIH][hapmap]
rs6712943	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6729513	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6739769	1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6757148	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71420778	0.96[EUR][1000 genomes]
rs7566741	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7567142	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7567267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7579121	0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7581628	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7581974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7583147	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7584039	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7593426	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7594368	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7595063	0.87[ASW][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7598071	0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9630977	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9631001	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9677274	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9677282	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9973317	0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9973465	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9973473	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9973633	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9973787	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9973848	0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10490028	ZDBF2	cis	cerebellum	SCAN
rs10490028	IKZF2	cis	cerebellum	SCAN
rs10490028	CREB1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210682000-210769600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:210725200-210737200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:210727800-210737400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:210733200-210791400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:210734800-210735600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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