Variant report

Variant	rs7617661
Chromosome Location	chr3:68190907-68190908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11706410	0.94[CHB][hapmap]
rs11709861	0.83[AMR][1000 genomes]
rs12486136	0.84[CHB][hapmap]
rs12486933	0.90[CHB][hapmap]
rs13076275	0.89[CHB][hapmap];0.81[YRI][hapmap]
rs13085628	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs4129248	0.84[CHB][hapmap]
rs6548962	0.90[CHB][hapmap]
rs6548984	0.90[CHB][hapmap];0.87[MKK][hapmap]
rs6548985	0.90[CHB][hapmap]
rs6548999	0.90[CHB][hapmap]
rs6549017	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6549020	0.90[CHB][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6768632	0.89[ASW][hapmap];0.80[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.80[AMR][1000 genomes]
rs6774687	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs7429303	0.82[CHB][hapmap]
rs7430480	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7433519	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs7622220	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7638117	0.82[AMR][1000 genomes]
rs9819989	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs9820035	0.83[AMR][1000 genomes]
rs9868432	0.83[ASW][hapmap];0.80[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2752014	chr3:68091879-68416989	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv1007450	chr3:68094416-68346546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv876925	chr3:68180422-68288626	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7617661	FAM19A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68190200-68193600	Enhancers	Fetal Brain Male	brain
2	chr3:68190800-68191800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:68190800-68192800	Enhancers	Brain Germinal Matrix	brain
4	chr3:68190800-68193400	Enhancers	Cortex derived primary cultured neurospheres	brain

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