Variant report

Variant	rs17391162
Chromosome Location	chr9:71402064-71402065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71398863..71402159-chr9:71407140..71410574,3	K562	blood:
2	chr9:71393697..71395796-chr9:71400941..71403104,3	K562	blood:
3	chr9:71400597..71404451-chr9:71406708..71409668,4	MCF-7	breast:
4	chr9:71395139..71397780-chr9:71401800..71403329,2	MCF-7	breast:
5	chr9:71401239..71403328-chr9:71403881..71406590,2	K562	blood:

Variant related genes	Relation type
ENSG00000187866	Chromatin interaction
ENSG00000236998	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10511964	0.80[CHD][hapmap];0.88[MEX][hapmap]
rs10511965	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10735625	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10746925	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10869422	0.83[MEX][hapmap]
rs11999960	0.84[AMR][1000 genomes]
rs12345874	0.82[CEU][hapmap]
rs12551225	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12555750	0.88[EUR][1000 genomes]
rs1537885	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17391596	0.82[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17391840	0.86[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17392861	0.84[AMR][1000 genomes]
rs17482181	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17482797	0.90[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17483533	0.83[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4120640	0.84[AMR][1000 genomes]
rs4745375	0.83[MEX][hapmap]
rs55671140	0.84[AMR][1000 genomes]
rs58220469	0.86[ASN][1000 genomes]
rs59031138	0.89[ASN][1000 genomes]
rs59550441	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61221055	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6560397	0.84[MEX][hapmap]
rs66460517	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66883415	0.80[AMR][1000 genomes]
rs67047473	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67457572	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018552	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]
rs7031263	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7044460	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72717927	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72717935	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72717955	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73457664	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7871676	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs8114	0.84[CHB][hapmap]
rs883951	0.87[MEX][hapmap]
rs945575	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs950785	0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs952590	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs972058	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs972059	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17391162	BGN	trans	cerebellum	SCAN
rs17391162	PIP5K1B	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71396000-71402400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr9:71396000-71403400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:71396000-71408200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:71396200-71409800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:71397200-71402200	Weak transcription	A549	lung
6	chr9:71397200-71403800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:71397200-71404200	Weak transcription	Esophagus	oesophagus
8	chr9:71397200-71409600	Weak transcription	Colonic Mucosa	Colon
9	chr9:71397200-71417400	Weak transcription	Lung	lung
10	chr9:71397800-71408000	Weak transcription	Gastric	stomach
11	chr9:71398600-71404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:71398600-71405400	Strong transcription	Primary B cells from cord blood	blood
13	chr9:71398800-71406000	Weak transcription	Spleen	Spleen
14	chr9:71398800-71408000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr9:71398800-71409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:71399000-71403000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:71399000-71403000	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:71399000-71403800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr9:71399000-71404000	Weak transcription	Ovary	ovary
20	chr9:71399000-71405600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:71399000-71406200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:71399000-71408400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:71399000-71408400	Weak transcription	Stomach Mucosa	stomach
24	chr9:71399000-71420200	Weak transcription	Fetal Stomach	stomach
25	chr9:71399200-71407800	Weak transcription	GM12878-XiMat	blood
26	chr9:71399400-71404800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:71399600-71403000	Weak transcription	HepG2	liver
28	chr9:71399600-71407200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:71399800-71413200	Weak transcription	Dnd41	blood
30	chr9:71400000-71403000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:71400200-71403000	Weak transcription	Fetal Intestine Large	intestine
32	chr9:71400200-71403000	Weak transcription	Psoas Muscle	Psoas
33	chr9:71400200-71403200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:71400200-71405800	Weak transcription	Brain Angular Gyrus	brain
35	chr9:71400200-71406000	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:71400400-71402800	Weak transcription	Thymus	Thymus
37	chr9:71400400-71403600	Weak transcription	Right Ventricle	heart
38	chr9:71400400-71404600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:71400400-71408000	Weak transcription	K562	blood
40	chr9:71400400-71408600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:71400600-71409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:71400800-71402600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr9:71400800-71402800	Weak transcription	Fetal Heart	heart
44	chr9:71400800-71403000	Weak transcription	Left Ventricle	heart
45	chr9:71400800-71403600	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:71400800-71403800	Weak transcription	Right Atrium	heart
47	chr9:71400800-71409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:71400800-71409000	Weak transcription	Adipose Nuclei	Adipose
49	chr9:71400800-71409000	Weak transcription	Small Intestine	intestine
50	chr9:71401000-71403200	Strong transcription	Primary monocytes fromperipheralblood	blood

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