Variant report

Variant	rs7018552
Chromosome Location	chr9:71406838-71406839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71392687..71396802-chr9:71403243..71407898,5	MCF-7	breast:
2	chr9:71400597..71404451-chr9:71406708..71409668,4	MCF-7	breast:
3	chr9:71394942..71397004-chr9:71406786..71409059,2	K562	blood:
4	chr9:71397068..71400120-chr9:71405362..71406999,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187866	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10114114	1.00[JPT][hapmap]
rs10511964	0.84[MEX][hapmap]
rs10511965	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10735625	0.83[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10746925	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11143602	1.00[JPT][hapmap]
rs11144133	0.80[MEX][hapmap]
rs11144167	0.81[AMR][1000 genomes]
rs11144206	1.00[JPT][hapmap]
rs11999960	0.84[AMR][1000 genomes]
rs12003432	1.00[JPT][hapmap]
rs12005037	1.00[JPT][hapmap]
rs12344543	1.00[JPT][hapmap]
rs12345874	0.82[CEU][hapmap]
rs12551225	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12555750	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1537885	1.00[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17059479	1.00[JPT][hapmap]
rs17391162	0.91[ASW][hapmap];0.95[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17391596	0.87[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17391840	0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17392861	0.84[AMR][1000 genomes]
rs17482181	1.00[CEU][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17482797	0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17483533	0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4120640	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4745375	1.00[JPT][hapmap];0.87[MEX][hapmap]
rs55671140	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55830509	0.81[AMR][1000 genomes]
rs59550441	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61221055	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6560397	0.80[MEX][hapmap]
rs66460517	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66883415	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67047473	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67457572	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7031263	0.83[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7044460	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7049222	0.81[CEU][hapmap]
rs72717927	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72717935	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72717955	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72720038	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73457664	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7871676	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs883951	0.91[MEX][hapmap]
rs945575	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs952590	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs972058	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs972059	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1050741	chr9:71405224-71450033	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv540148	chr9:71405224-71450033	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7018552	BGN	trans	cerebellum	SCAN
rs7018552	PIP5K1B	cis	Artery Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71396000-71408200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:71396200-71409800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:71397200-71409600	Weak transcription	Colonic Mucosa	Colon
4	chr9:71397200-71417400	Weak transcription	Lung	lung
5	chr9:71397800-71408000	Weak transcription	Gastric	stomach
6	chr9:71398800-71408000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:71398800-71409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:71399000-71408400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:71399000-71408400	Weak transcription	Stomach Mucosa	stomach
10	chr9:71399000-71420200	Weak transcription	Fetal Stomach	stomach
11	chr9:71399200-71407800	Weak transcription	GM12878-XiMat	blood
12	chr9:71399600-71407200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:71399800-71413200	Weak transcription	Dnd41	blood
14	chr9:71400400-71408000	Weak transcription	K562	blood
15	chr9:71400400-71408600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:71400600-71409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:71400800-71409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:71400800-71409000	Weak transcription	Adipose Nuclei	Adipose
19	chr9:71400800-71409000	Weak transcription	Small Intestine	intestine
20	chr9:71401000-71407000	Weak transcription	Brain Germinal Matrix	brain
21	chr9:71402600-71413400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:71402600-71413600	Weak transcription	Primary T cells from cord blood	blood
23	chr9:71403200-71407200	Weak transcription	Placenta	Placenta
24	chr9:71403200-71419800	Weak transcription	Pancreas	Pancrea
25	chr9:71404200-71408400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:71404400-71409800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:71404600-71408600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:71404600-71408800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:71404600-71408800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr9:71404600-71431400	Weak transcription	HepG2	liver
31	chr9:71404800-71408200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:71404800-71408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:71404800-71408800	Weak transcription	Fetal Intestine Large	intestine
34	chr9:71404800-71413200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:71405000-71408200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr9:71405000-71408200	Weak transcription	Fetal Intestine Small	intestine
37	chr9:71405400-71407000	Enhancers	Aorta	Aorta
38	chr9:71405400-71407000	Enhancers	Fetal Heart	heart
39	chr9:71405400-71408400	Weak transcription	Primary B cells from cord blood	blood
40	chr9:71405600-71408200	Weak transcription	Right Ventricle	heart
41	chr9:71406200-71407000	Enhancers	Left Ventricle	heart
42	chr9:71406200-71408400	Weak transcription	Right Atrium	heart
43	chr9:71406800-71407000	Enhancers	Psoas Muscle	Psoas

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