Variant report

Variant	rs10490522
Chromosome Location	chr2:152186147-152186148
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	chr2:152184657..152187504-chr2:152188259..152189989,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10167886	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10174715	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10176271	0.89[EUR][1000 genomes]
rs1023634	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11679466	0.80[EUR][1000 genomes]
rs12617724	0.81[EUR][1000 genomes]
rs2278089	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs289828	0.88[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs289829	0.86[GIH][hapmap]
rs289835	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34132424	0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap]
rs3771886	0.84[GIH][hapmap]
rs3771887	0.86[GIH][hapmap]
rs3771888	0.86[GIH][hapmap]
rs387297	0.83[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3936325	0.85[ASN][1000 genomes]
rs4664021	0.99[ASN][1000 genomes]
rs4664357	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6433327	0.81[CHB][hapmap]
rs6708382	0.81[CHB][hapmap]
rs6715393	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6715902	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6719213	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6726634	0.81[CHB][hapmap]
rs6747782	0.86[GIH][hapmap]
rs6751802	0.86[GIH][hapmap]
rs7574216	0.99[ASN][1000 genomes]
rs7585805	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9287955	0.81[CHB][hapmap]
rs9287956	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10490522	STAM2	cis	parietal	SCAN
rs10490522	RIF1	cis	parietal	SCAN
rs10490522	TNFAIP6	cis	brain	BrainEAC
rs10490522	TNFAIP6	cis	Whole Blood	GTEx
rs10490522	RND3	cis	cerebellum	SCAN
rs10490522	RBM43	cis	brain	BrainEAC
rs10490522	TNFAIP6	cis	hippocampus	BrainEAC
rs10490522	RBM43	cis	parietal	SCAN
rs10490522	TNFAIP6	cis	parietal	SCAN
rs10490522	NMI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152186000-152188800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:152186000-152190400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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