Variant report

Variant	rs4946312
Chromosome Location	chr6:118310478-118310479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13198431	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13211121	0.88[AMR][1000 genomes]
rs1338971	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17079625	0.83[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2211099	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2355798	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34358304	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34729097	0.85[AMR][1000 genomes]
rs36172496	0.83[EUR][1000 genomes]
rs4113075	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4120871	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4245490	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4434501	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4945604	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5002415	0.87[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs6914871	0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6928714	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6935258	0.85[AMR][1000 genomes]
rs6935516	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs7744988	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9374693	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374698	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9387532	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9401043	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9401045	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9481751	0.87[CEU][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs9766457	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9968789	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4946312	SLC35F1	cis	cerebellum	SCAN
rs4946312	PLN	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118305600-118315400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr6:118308200-118311400	Weak transcription	Brain Angular Gyrus	brain
3	chr6:118308400-118314200	Weak transcription	Fetal Brain Female	brain
4	chr6:118308600-118311400	Weak transcription	Fetal Brain Male	brain
5	chr6:118309200-118315200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:118309800-118312200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:118309800-118312200	Enhancers	Brain Substantia Nigra	brain
8	chr6:118310000-118312000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr6:118310000-118312800	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:118310000-118315200	Enhancers	Brain Hippocampus Middle	brain
11	chr6:118310200-118310800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:118310200-118312000	Enhancers	Brain Germinal Matrix	brain
13	chr6:118310400-118310600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:118310400-118310600	Enhancers	Brain Anterior Caudate	brain
15	chr6:118310400-118310800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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