Variant report

Variant	rs1894612
Chromosome Location	chr6:118482161-118482162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1113896	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13210032	0.85[CEU][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1334828	0.85[CEU][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1573713	0.85[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573714	0.85[CEU][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1573715	0.85[CEU][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2356075	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484150	0.85[CEU][hapmap]
rs34008090	0.86[ASN][1000 genomes]
rs4636058	0.85[CEU][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4945612	0.93[ASN][1000 genomes]
rs743927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743928	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763098	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320642	0.83[CEU][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9374717	0.81[JPT][hapmap]
rs9374719	0.93[ASN][1000 genomes]
rs9385036	0.84[CEU][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9387553	0.86[JPT][hapmap]
rs9398484	0.85[CEU][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9481767	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9489307	0.86[ASN][1000 genomes]
rs9489310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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
2	nsv428153	chr6:118430517-118586974	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1030089	chr6:118436482-118604516	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538427	chr6:118436482-118604516	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1894612	SLC35F1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118468000-118485000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:118476800-118485800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:118477000-118484200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:118478400-118484800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:118481200-118484400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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