Variant report

Variant	rs6676033
Chromosome Location	chr1:220075775-220075776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10863513	0.94[ASW][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs11118455	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs13374441	0.87[AFR][1000 genomes]
rs2378330	0.85[LWK][hapmap];0.84[MKK][hapmap]
rs6694002	0.94[ASW][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs6698689	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74139229	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006393	chr1:219925261-220126458	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1067840	chr1:219990803-220091941	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6676033	SPATA17	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220074000-220076200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:220074800-220076200	Enhancers	K562	blood
3	chr1:220075200-220077400	Enhancers	Duodenum Mucosa	Duodenum
4	chr1:220075400-220077000	Enhancers	HepG2	liver
5	chr1:220075600-220077400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:220075600-220077400	Enhancers	Fetal Intestine Large	intestine
7	chr1:220075600-220077400	Enhancers	Fetal Intestine Small	intestine

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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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