Variant report

Variant	rs9398476
Chromosome Location	chr6:118343350-118343351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:118334788..118337364-chr6:118342018..118344547,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11153713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153717	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs11153718	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs12190596	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12206104	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12206792	0.88[CHB][hapmap]
rs12207545	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs12208166	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12208433	0.82[CEU][hapmap]
rs12213071	0.81[CEU][hapmap]
rs1338968	0.81[CHB][hapmap]
rs1547754	0.86[CEU][hapmap];0.80[MEX][hapmap]
rs4132664	0.90[CEU][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4245492	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs4283912	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4373391	0.90[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4479971	0.90[CEU][hapmap]
rs4945608	0.81[EUR][1000 genomes]
rs6900812	0.85[EUR][1000 genomes]
rs9320626	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9320627	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9320628	0.82[EUR][1000 genomes]
rs9320629	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9320630	0.82[EUR][1000 genomes]
rs9320634	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9372494	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9374700	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs9374704	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs9374709	0.86[CEU][hapmap]
rs9374711	0.93[CEU][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9385027	0.88[CHB][hapmap]
rs9385029	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9387535	0.82[CHB][hapmap]
rs9387537	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387539	0.82[EUR][1000 genomes]
rs9387547	0.93[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9398474	0.86[CEU][hapmap]
rs9398475	0.92[EUR][1000 genomes]
rs9398477	0.86[CEU][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9401040	0.87[CHB][hapmap]
rs9401044	0.88[CHB][hapmap]
rs9401046	0.87[CHB][hapmap]
rs9401047	0.86[CEU][hapmap]
rs9401049	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9401050	0.80[EUR][1000 genomes]
rs9401051	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9401052	0.90[CEU][hapmap]
rs9489295	0.88[CHB][hapmap]

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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9398476	MICAL3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118338800-118344400	Weak transcription	Fetal Brain Female	brain
2	chr6:118338800-118352400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:118339000-118347200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:118343200-118343400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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