Variant report

Variant	rs57467578
Chromosome Location	chr9:15512821-15512822
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	TBP	chr9:15512457-15513800	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr9:15512774-15513292	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFIC	chr9:15512086-15513083	GM12878	blood:	n/a	n/a
4	SP1	chr9:15512743-15513324	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:15511947-15513893	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr9:15512444-15513786	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr9:15512115-15513907	H1-hESC	embryonic stem cell:	n/a	n/a
8	SREBP1	chr9:15510259-15513935	GM12878	blood:	n/a	n/a
9	CHD1	chr9:15509050-15513782	H1-hESC	embryonic stem cell:	n/a	chr9:15510554-15510564 chr9:15510784-15510794 chr9:15510444-15510454 chr9:15511226-15511236
10	CHD1	chr9:15508987-15513035	GM12878	blood:	n/a	chr9:15510554-15510564 chr9:15510784-15510794 chr9:15510444-15510454 chr9:15511226-15511236
11	POLR2A	chr9:15512780-15512901	MCF10A-Er-Src	breast:	n/a	n/a
12	ZEB1	chr9:15512515-15512850	GM12878	blood:	n/a	chr9:15512651-15512660 chr9:15512636-15512645

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15512114..15513693-chr9:15523609..15526046,2	MCF-7	breast:
2	chr9:15511224..15513667-chr9:15516724..15518268,2	K562	blood:

Variant related genes	Relation type
PSIP1	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10124624	0.83[ASN][1000 genomes]
rs10283923	0.91[ASN][1000 genomes]
rs10283927	0.91[ASN][1000 genomes]
rs12336503	0.91[ASN][1000 genomes]
rs12336509	0.91[ASN][1000 genomes]
rs12339417	0.91[ASN][1000 genomes]
rs12682808	0.85[ASN][1000 genomes]
rs12683553	0.90[ASN][1000 genomes]
rs12686545	0.83[ASN][1000 genomes]
rs16933311	0.91[ASN][1000 genomes]
rs16933320	0.87[ASN][1000 genomes]
rs16933348	1.00[ASN][1000 genomes]
rs16933350	0.80[EUR][1000 genomes]
rs1828382	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1828383	0.83[ASN][1000 genomes]
rs2175257	0.91[ASN][1000 genomes]
rs2277191	0.90[ASN][1000 genomes]
rs2777950	0.89[ASN][1000 genomes]
rs28537229	0.88[ASN][1000 genomes]
rs55771541	0.96[ASN][1000 genomes]
rs56361298	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57142629	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57191285	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57849124	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58607272	0.83[ASN][1000 genomes]
rs58915725	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59520337	0.80[EUR][1000 genomes]
rs59639757	0.96[ASN][1000 genomes]
rs62571010	0.91[ASN][1000 genomes]
rs62571018	0.80[EUR][1000 genomes]
rs62571021	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571022	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62571023	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62571024	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62571027	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62571029	0.80[EUR][1000 genomes]
rs62571030	0.84[ASN][1000 genomes]
rs62571031	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62571032	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6474927	0.84[ASN][1000 genomes]
rs7018658	0.91[ASN][1000 genomes]
rs7021153	0.87[ASN][1000 genomes]
rs7023730	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73408328	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408340	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73410253	0.83[ASN][1000 genomes]
rs73410254	0.83[ASN][1000 genomes]
rs73644657	0.84[ASN][1000 genomes]
rs7852774	0.83[ASN][1000 genomes]
rs7856710	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7857933	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7863046	0.84[ASN][1000 genomes]
rs7863139	0.91[EUR][1000 genomes];0.91[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	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription 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 target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57467578	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15508600-15513200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr9:15511400-15513600	Flanking Active TSS	GM12878-XiMat	blood
3	chr9:15511600-15513000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr9:15511600-15513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:15511600-15513200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:15511800-15513000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:15511800-15513000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr9:15511800-15513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:15511800-15513400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr9:15511800-15513400	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr9:15511800-15513600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr9:15511800-15513600	Enhancers	Primary T cells from cord blood	blood
13	chr9:15511800-15513600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr9:15511800-15513600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr9:15511800-15513800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr9:15511800-15513800	Enhancers	Primary B cells from cord blood	blood
17	chr9:15511800-15513800	Enhancers	Primary B cells from peripheral blood	blood
18	chr9:15511800-15513800	Enhancers	Primary hematopoietic stem cells	blood
19	chr9:15511800-15513800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr9:15511800-15513800	Enhancers	Fetal Thymus	thymus
21	chr9:15512000-15513000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr9:15512000-15513000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr9:15512000-15513200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:15512000-15513400	Enhancers	Brain Germinal Matrix	brain
25	chr9:15512200-15513400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:15512400-15513200	Weak transcription	Fetal Brain Female	brain
27	chr9:15512400-15513200	Enhancers	K562	blood
28	chr9:15512400-15513400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:15512400-15513400	Weak transcription	A549	lung
30	chr9:15512400-15515000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:15512600-15513600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:15512600-15513600	Weak transcription	Thymus	Thymus
33	chr9:15512600-15514200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:15512800-15513200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:15512800-15513200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr9:15512800-15513200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr9:15512800-15513200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr9:15512800-15513200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr9:15512800-15513400	Active TSS	H1 Cell Line	embryonic stem cell
40	chr9:15512800-15513800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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