Variant report

Variant	rs11903855
Chromosome Location	chr2:86630752-86630753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86630182..86633982-chr2:86666784..86669925,4	MCF-7	breast:
2	chr2:86630213..86633133-chr2:86645838..86647616,2	MCF-7	breast:
3	chr2:86630490..86633465-chr2:86635525..86637778,2	MCF-7	breast:
4	chr2:86629640..86632102-chr2:86632580..86634181,2	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10185085	1.00[CHB][hapmap]
rs1033288	1.00[ASN][1000 genomes]
rs1033289	1.00[ASN][1000 genomes]
rs1036940	1.00[CHB][hapmap]
rs11127040	1.00[CHB][hapmap]
rs11127042	1.00[CHB][hapmap]
rs11678201	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11687162	1.00[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11693352	1.00[CHB][hapmap]
rs12714182	0.88[CEU][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12714185	1.00[CHB][hapmap]
rs12714187	1.00[CHB][hapmap]
rs12995117	1.00[CHB][hapmap]
rs1468039	1.00[CHB][hapmap]
rs1518811	1.00[CHB][hapmap]
rs1964087	0.89[ASN][1000 genomes]
rs1964088	0.96[ASN][1000 genomes]
rs2030259	1.00[CHB][hapmap]
rs2044230	1.00[CHB][hapmap]
rs2113607	0.88[CEU][hapmap]
rs2113608	0.89[ASN][1000 genomes]
rs2113609	0.89[ASN][1000 genomes]
rs2367238	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3952742	0.83[ASN][1000 genomes]
rs4832278	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs4832281	0.89[ASN][1000 genomes]
rs4832283	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832285	1.00[CHB][hapmap]
rs4832289	1.00[CHB][hapmap]
rs4832294	1.00[CHB][hapmap]
rs6547680	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708398	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6713586	0.88[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6714826	1.00[CHB][hapmap]
rs6718850	0.83[MEX][hapmap]
rs6720331	1.00[ASN][1000 genomes]
rs6736462	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6756146	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7573005	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574389	1.00[CHB][hapmap]
rs908789	1.00[ASN][1000 genomes]
rs950780	1.00[CHB][hapmap]
rs966477	1.00[CHB][hapmap]

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11903855	RNF103	cis	cerebellum	SCAN
rs11903855	PTCD3	cis	cerebellum	SCAN
rs11903855	ST3GAL5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86621600-86631000	Weak transcription	Gastric	stomach

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