Variant report

Variant	rs7044045
Chromosome Location	chr9:71355133-71355134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr9:71354628-71355203	HepG2	liver:	n/a	n/a
2	ZEB1	chr9:71354501-71355210	HepG2	liver:	n/a	n/a
3	MYBL2	chr9:71354526-71355542	HepG2	liver:	n/a	n/a
4	SP1	chr9:71354525-71355204	HepG2	liver:	n/a	n/a
5	HEY1	chr9:71354544-71355199	HepG2	liver:	n/a	n/a
6	ZEB1	chr9:71354460-71355318	HepG2	liver:	n/a	n/a
7	EP300	chr9:71354655-71355149	HepG2	liver:	n/a	n/a
8	RAD21	chr9:71354578-71355195	HepG2	liver:	n/a	n/a
9	MYBL2	chr9:71354601-71355259	HepG2	liver:	n/a	n/a
10	MBD4	chr9:71354547-71355179	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:71354491-71355203	HepG2	liver:	n/a	n/a
12	MAX	chr9:71354476-71355202	HepG2	liver:	n/a	chr9:71354699-71354708
13	TBP	chr9:71354677-71355149	HepG2	liver:	n/a	n/a
14	RAD21	chr9:71354713-71355152	HepG2	liver:	n/a	n/a
15	TEAD4	chr9:71354336-71355769	HepG2	liver:	n/a	n/a
16	NFIC	chr9:71354469-71355192	HepG2	liver:	n/a	n/a
17	HDAC2	chr9:71354579-71355169	HepG2	liver:	n/a	chr9:71354900-71354909
18	EP300	chr9:71354392-71355251	HepG2	liver:	n/a	chr9:71354545-71354559

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71318947..71321633-chr9:71353997..71355633,2	MCF-7	breast:

Variant related genes	Relation type
PIP5K1B	TF binding region
ENSG00000107242	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11143572	0.85[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11143589	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11789971	0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12682815	0.83[AFR][1000 genomes]
rs12686355	0.88[ASW][hapmap];0.87[LWK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs13296679	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs34414551	0.89[ASN][1000 genomes]
rs35213801	0.85[ASN][1000 genomes]
rs7032100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7043892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7044032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7044422	0.90[LWK][hapmap];0.95[YRI][hapmap]
rs7866673	0.83[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026962	chr9:71130848-71357605	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv893415	chr9:71347988-71364351	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7044045	PGM5	cis	parietal	SCAN
rs7044045	MAMDC2	cis	parietal	SCAN
rs7044045	GALNT4	trans	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71343400-71363000	Weak transcription	GM12878-XiMat	blood
2	chr9:71343800-71357200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr9:71347400-71357800	Weak transcription	Primary B cells from cord blood	blood
4	chr9:71348200-71359000	Weak transcription	Lung	lung
5	chr9:71350000-71356600	Weak transcription	Aorta	Aorta
6	chr9:71351000-71370600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:71351200-71355800	Enhancers	Fetal Intestine Small	intestine
8	chr9:71351200-71360000	Weak transcription	Gastric	stomach
9	chr9:71352400-71365800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:71353400-71355200	Enhancers	Right Atrium	heart
11	chr9:71353400-71356600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:71353600-71355200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr9:71353600-71355600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr9:71353800-71356200	Weak transcription	Colonic Mucosa	Colon
15	chr9:71354000-71355400	Enhancers	Primary hematopoietic stem cells	blood
16	chr9:71354000-71356400	Weak transcription	Small Intestine	intestine
17	chr9:71354400-71355600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr9:71354400-71356400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:71354400-71356800	Enhancers	Left Ventricle	heart
20	chr9:71354400-71356800	Enhancers	Pancreas	Pancrea
21	chr9:71354600-71355200	Enhancers	Placenta	Placenta
22	chr9:71354600-71355400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr9:71354600-71355400	Active TSS	Rectal Smooth Muscle	rectum
24	chr9:71354600-71356000	Flanking Active TSS	HepG2	liver
25	chr9:71354600-71357200	Enhancers	K562	blood
26	chr9:71354800-71356200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr9:71354800-71361600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:71355000-71355400	Active TSS	Duodenum Mucosa	Duodenum
29	chr9:71355000-71355400	Flanking Active TSS	Fetal Heart	heart
30	chr9:71355000-71355600	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr9:71355000-71355600	Active TSS	Stomach Mucosa	stomach
32	chr9:71355000-71356000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr9:71355000-71356200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:71355000-71356800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:71355000-71359000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:71355000-71359400	Weak transcription	Right Ventricle	heart
37	chr9:71355000-71360000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:71355000-71362000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr9:71355000-71364400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr9:71355000-71365400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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