Variant report

Variant	rs16825274
Chromosome Location	chr3:155408234-155408235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10513482	0.87[CEU][hapmap]
rs13082172	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1850848	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850849	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441007	0.87[CEU][hapmap]
rs6808225	0.87[CEU][hapmap]
rs7610374	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs7636687	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7636703	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7639887	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7651444	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16825274	SCHIP1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155395000-155416800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:155395200-155412000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:155400600-155408800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
6	chr3:155400800-155418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:155401000-155408800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:155404600-155408400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:155406400-155408600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:155408000-155411800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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