Variant report

Variant	rs550879
Chromosome Location	chr17:67368443-67368444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67367554..67369166-chr17:67520800..67522468,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1642220	0.82[CHB][hapmap]
rs1662694	0.88[ASN][1000 genomes]
rs182834	0.88[ASN][1000 genomes]
rs2430763	0.86[ASN][1000 genomes]
rs2430764	0.91[ASN][1000 genomes]
rs2592208	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2592209	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs333910	0.85[ASN][1000 genomes]
rs333911	0.88[ASN][1000 genomes]
rs333912	0.87[ASN][1000 genomes]
rs333913	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs333914	0.88[ASN][1000 genomes]
rs333915	0.88[ASN][1000 genomes]
rs333916	0.91[CHB][hapmap];0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs333917	0.91[CHB][hapmap];0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs333918	0.88[ASN][1000 genomes]
rs333919	0.85[ASN][1000 genomes]
rs474246	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs475278	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs489695	0.88[ASN][1000 genomes]
rs491516	0.88[ASN][1000 genomes]
rs4968791	0.84[ASN][1000 genomes]
rs497012	0.98[ASN][1000 genomes]
rs536108	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs569063	0.88[ASN][1000 genomes]
rs575988	0.85[ASN][1000 genomes]
rs58235597	0.88[ASN][1000 genomes]
rs6501323	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs707246	0.84[ASN][1000 genomes]
rs707247	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs817103	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs817543	0.91[CHB][hapmap]
rs817545	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs817546	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs817556	0.80[JPT][hapmap]
rs817565	0.80[JPT][hapmap]
rs817566	0.81[JPT][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	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs550879	AXIN2	cis	cerebellum	SCAN
rs550879	TEX2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67367400-67368600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr17:67367400-67368600	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr17:67367600-67368600	Enhancers	H9 Cell Line	embryonic stem cell
4	chr17:67367600-67368600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr17:67367800-67368600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:67368000-67369400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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