Variant report

Variant	rs9976609
Chromosome Location	chr21:37897709-37897710
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:37896121..37897904-chr21:37913611..37915970,2	MCF-7	breast:
2	chr21:37896205..37897774-chr21:38337593..38339393,2	K562	blood:
3	chr21:37897297..37900061-chr21:37900789..37903284,3	K562	blood:

Variant related genes	Relation type
ENSG00000159261	Chromatin interaction
ENSG00000159267	Chromatin interaction
ENSG00000224790	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11088353	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088354	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2000547	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2070518	0.97[ASN][1000 genomes]
rs2187302	0.88[ASN][1000 genomes]
rs2187303	0.85[ASN][1000 genomes]
rs364698	0.91[EUR][1000 genomes]
rs364846	0.91[EUR][1000 genomes]
rs364916	0.91[EUR][1000 genomes]
rs365416	0.91[EUR][1000 genomes]
rs366381	0.91[EUR][1000 genomes]
rs367166	0.88[JPT][hapmap]
rs371945	0.80[EUR][1000 genomes]
rs372213	0.80[EUR][1000 genomes]
rs375572	0.91[EUR][1000 genomes]
rs375662	0.91[EUR][1000 genomes]
rs376590	0.80[EUR][1000 genomes]
rs377160	0.80[EUR][1000 genomes]
rs377527	0.80[EUR][1000 genomes]
rs377574	0.80[EUR][1000 genomes]
rs382635	0.80[EUR][1000 genomes]
rs382937	0.80[EUR][1000 genomes]
rs383609	0.80[EUR][1000 genomes]
rs387842	0.80[EUR][1000 genomes]
rs390432	0.91[EUR][1000 genomes]
rs393851	0.80[EUR][1000 genomes]
rs394087	0.80[EUR][1000 genomes]
rs394110	0.80[EUR][1000 genomes]
rs394211	0.80[EUR][1000 genomes]
rs395383	0.80[EUR][1000 genomes]
rs397990	0.80[EUR][1000 genomes]
rs397996	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs398591	0.88[JPT][hapmap]
rs399522	0.80[EUR][1000 genomes]
rs399711	0.89[JPT][hapmap]
rs400019	0.89[JPT][hapmap]
rs400267	0.94[JPT][hapmap]
rs400544	0.89[JPT][hapmap]
rs405901	0.80[EUR][1000 genomes]
rs409231	0.80[EUR][1000 genomes]
rs412775	0.89[JPT][hapmap]
rs413616	0.89[JPT][hapmap]
rs413852	0.80[EUR][1000 genomes]
rs414911	0.80[EUR][1000 genomes]
rs415100	0.80[EUR][1000 genomes]
rs415124	0.80[EUR][1000 genomes]
rs416875	0.90[EUR][1000 genomes]
rs417173	0.80[EUR][1000 genomes]
rs417191	0.91[EUR][1000 genomes]
rs419941	0.80[EUR][1000 genomes]
rs420925	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs425864	0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs428948	0.80[EUR][1000 genomes]
rs429326	0.80[EUR][1000 genomes]
rs431530	0.89[JPT][hapmap]
rs439888	0.87[JPT][hapmap]
rs440551	0.80[EUR][1000 genomes]
rs443968	0.88[JPT][hapmap]
rs445103	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs447759	0.91[EUR][1000 genomes]
rs448014	0.80[EUR][1000 genomes]
rs448332	0.89[JPT][hapmap]
rs448482	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs448659	0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs448687	0.89[JPT][hapmap]
rs448849	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs450183	0.80[EUR][1000 genomes]
rs451243	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs451614	0.80[EUR][1000 genomes]
rs452072	0.85[EUR][1000 genomes]
rs452081	0.91[EUR][1000 genomes]
rs452107	0.80[EUR][1000 genomes]
rs452128	0.89[EUR][1000 genomes]
rs4816539	0.97[ASN][1000 genomes]
rs6517359	0.95[ASN][1000 genomes]
rs7281531	0.97[ASN][1000 genomes]
rs7282508	0.98[ASN][1000 genomes]
rs7510508	0.91[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928839	0.80[ASN][1000 genomes]
rs97959	0.90[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	nsv834090	chr21:37812545-38009542	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1064290	chr21:37878964-37983133	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9976609	OLIG2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:37893800-37897800	Enhancers	Fetal Muscle Leg	muscle
2	chr21:37894800-37898800	Weak transcription	Right Atrium	heart
3	chr21:37895800-37902600	Weak transcription	GM12878-XiMat	blood
4	chr21:37897000-37911600	Weak transcription	Pancreas	Pancrea
5	chr21:37897600-37902200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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