Variant report

Variant	rs16825229
Chromosome Location	chr3:155386745-155386746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10212594	0.84[CEU][hapmap]
rs11707005	0.84[CEU][hapmap]
rs12638480	0.83[CEU][hapmap]
rs13314098	0.84[CEU][hapmap]
rs13317911	0.84[CEU][hapmap]
rs13326969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13327502	0.84[CEU][hapmap]
rs16825208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16825256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17411990	1.00[CEU][hapmap]
rs1850847	0.84[CEU][hapmap]
rs2304406	0.84[CEU][hapmap]
rs4425301	0.84[CEU][hapmap]
rs4679751	0.84[CEU][hapmap]
rs4680193	0.84[CEU][hapmap]
rs4680195	0.84[CEU][hapmap]
rs4680197	0.84[CEU][hapmap]
rs4680202	0.91[CEU][hapmap]
rs4680206	0.84[CEU][hapmap]
rs4680207	0.84[CEU][hapmap]
rs56007034	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62286076	0.91[EUR][1000 genomes]
rs6783986	0.84[CEU][hapmap]
rs6787497	0.81[AMR][1000 genomes]
rs6795967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6802895	0.84[CEU][hapmap]
rs6807243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6807368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808145	0.84[CEU][hapmap]
rs7637459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7644232	0.84[CEU][hapmap]
rs925967	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs932207	0.84[CEU][hapmap]
rs932208	0.84[CEU][hapmap]
rs9814642	0.84[CEU][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap]
rs9823723	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs9829178	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9851365	0.83[CEU][hapmap]
rs9866635	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9870721	0.84[CEU][hapmap];0.94[GIH][hapmap];0.81[TSI][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	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16825229	SLC33A1	cis	cerebellum	SCAN
rs16825229	SCARNA7	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155383400-155387000	Enhancers	HepG2	liver
2	chr3:155383400-155390200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155383400-155393800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:155383400-155394000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:155383400-155395800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:155383600-155394000	Weak transcription	Pancreas	Pancrea
7	chr3:155385200-155394000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:155385400-155390000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:155386200-155390000	Weak transcription	Fetal Intestine Small	intestine

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