Variant report

Variant	rs9353446
Chromosome Location	chr6:87780724-87780725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1983841	0.92[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2025486	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3828759	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4706287	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6454578	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6926846	0.92[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7751610	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9342104	0.88[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9444470	0.92[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9444471	0.87[AMR][1000 genomes];0.89[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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9353446	C6orf162	cis	cerebellum	SCAN
rs9353446	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9353446	SLC35A1	cis	multi-tissue	Pritchard
rs9353446	C6orf162	cis	parietal	SCAN
rs9353446	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87769000-87784000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:87779800-87781600	Enhancers	Duodenum Mucosa	Duodenum
3	chr6:87779800-87781600	Enhancers	Fetal Intestine Large	intestine
4	chr6:87779800-87785200	Enhancers	Fetal Intestine Small	intestine
5	chr6:87780200-87781000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:87780400-87784000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:87780600-87780800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:87780600-87780800	Enhancers	Hela-S3	cervix
9	chr6:87780600-87783600	Weak transcription	Stomach Mucosa	stomach
10	chr6:87780600-87784000	Weak transcription	Rectal Mucosa Donor 29	rectum

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Input of quick search could be:

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

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