Variant report

Variant	rs11717902
Chromosome Location	chr3:133392910-133392911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133380517..133382268-chr3:133392031..133394854,2	MCF-7	breast:
2	chr3:133391131..133393596-chr3:133524398..133526804,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163781	Chromatin interaction
ENSG00000242337	Chromatin interaction
ENSG00000144867	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10512903	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512904	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512907	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512908	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512909	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512913	1.00[LWK][hapmap]
rs11706413	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706586	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706809	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707750	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708197	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708532	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708565	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709132	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709349	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709404	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709461	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11709940	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710111	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710717	1.00[ASN][1000 genomes]
rs11711706	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712186	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11712672	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713205	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713248	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714392	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714422	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715407	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715435	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715615	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716197	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716388	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716415	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717424	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718050	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718234	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718255	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719366	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719585	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719687	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720825	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13093428	1.00[LWK][hapmap]
rs16840594	0.85[EUR][1000 genomes]
rs16840595	0.88[EUR][1000 genomes]
rs17301253	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17301521	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17301766	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17301889	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373504	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373726	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718801	0.94[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28846461	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55729127	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55741097	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040719	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56292037	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56323915	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280563	0.82[AMR][1000 genomes]
rs62282385	0.81[AMR][1000 genomes]
rs62282388	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282389	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282390	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282392	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282415	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282417	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282418	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282419	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282420	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282421	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282424	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282425	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282427	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282428	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282429	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282431	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282451	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282452	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282453	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282454	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282456	0.90[EUR][1000 genomes]
rs62284060	0.82[AMR][1000 genomes]
rs6765265	0.86[EUR][1000 genomes]
rs7349558	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628914	0.81[CEU][hapmap]
rs7630957	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs7650725	0.90[EUR][1000 genomes]
rs7653808	0.90[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11717902	TOPBP1	cis	cerebellum	SCAN
rs11717902	ACPP	cis	parietal	SCAN
rs11717902	TOPBP1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133387800-133393000	Weak transcription	Right Atrium	heart
2	chr3:133389400-133394600	Enhancers	HepG2	liver
3	chr3:133389800-133393200	Weak transcription	Gastric	stomach
4	chr3:133390600-133393200	Weak transcription	Pancreas	Pancrea
5	chr3:133392400-133393800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:133392800-133393000	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
7	chr3:133392800-133393000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr3:133392800-133393000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:133392800-133393000	Enhancers	Brain Anterior Caudate	brain
10	chr3:133392800-133393000	Bivalent Enhancer	Brain Germinal Matrix	brain
11	chr3:133392800-133393000	Bivalent Enhancer	Brain Hippocampus Middle	brain
12	chr3:133392800-133393000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr3:133392800-133393200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr3:133392800-133393200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:133392800-133393200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:133392800-133393200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr3:133392800-133393200	Enhancers	Brain Substantia Nigra	brain
18	chr3:133392800-133393200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr3:133392800-133393200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr3:133392800-133393200	Bivalent/Poised TSS	Right Ventricle	heart
21	chr3:133392800-133393600	Flanking Active TSS	Liver	Liver
22	chr3:133392800-133393600	Active TSS	Brain Angular Gyrus	brain
23	chr3:133392800-133393800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:133392800-133393800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr3:133392800-133393800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:133392800-133393800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:133392800-133393800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:133392800-133393800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:133392800-133394000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr3:133392800-133394000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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