Variant report

Variant	rs62571017
Chromosome Location	chr9:15509963-15509964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:
2	chr9:15507256..15510187-chr9:15510704..15514473,5	K562	blood:

Variant related genes	Relation type
ENSG00000164989	Chromatin interaction
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs16933296	0.85[EUR][1000 genomes]
rs16933350	0.95[EUR][1000 genomes]
rs1828382	0.81[EUR][1000 genomes]
rs3087653	0.90[EUR][1000 genomes]
rs41268961	0.90[EUR][1000 genomes]
rs41306098	0.90[EUR][1000 genomes]
rs55649599	0.84[EUR][1000 genomes]
rs57142629	0.81[EUR][1000 genomes]
rs58915725	0.81[EUR][1000 genomes]
rs59355275	1.00[EUR][1000 genomes]
rs59520337	0.95[EUR][1000 genomes]
rs62570969	0.85[EUR][1000 genomes]
rs62570970	0.80[EUR][1000 genomes]
rs62570971	0.80[EUR][1000 genomes]
rs62570972	0.85[EUR][1000 genomes]
rs62570973	0.80[EUR][1000 genomes]
rs62570974	0.80[EUR][1000 genomes]
rs62570975	0.80[EUR][1000 genomes]
rs62570976	0.85[EUR][1000 genomes]
rs62570980	0.90[EUR][1000 genomes]
rs62570991	0.90[EUR][1000 genomes]
rs62570992	0.90[EUR][1000 genomes]
rs62570993	0.90[EUR][1000 genomes]
rs62571001	0.85[EUR][1000 genomes]
rs62571002	0.85[EUR][1000 genomes]
rs62571003	0.87[EUR][1000 genomes]
rs62571007	0.90[EUR][1000 genomes]
rs62571008	0.87[EUR][1000 genomes]
rs62571009	0.90[EUR][1000 genomes]
rs62571011	0.90[EUR][1000 genomes]
rs62571015	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571016	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571018	0.95[EUR][1000 genomes]
rs62571029	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571031	0.81[EUR][1000 genomes]
rs62571032	0.81[EUR][1000 genomes]
rs62571033	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571037	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62571046	0.95[EUR][1000 genomes]
rs62571047	0.95[EUR][1000 genomes]
rs62571048	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571050	0.92[EUR][1000 genomes]
rs62571051	0.90[EUR][1000 genomes]
rs62571052	0.87[EUR][1000 genomes]
rs7023730	0.81[EUR][1000 genomes]
rs7856523	0.95[EUR][1000 genomes]
rs7856657	0.93[EUR][1000 genomes]
rs7856710	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3440011	chr9:15509577-15512125	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62571017	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
2	chr9:15476600-15510000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:15493000-15510000	Weak transcription	Gastric	stomach
4	chr9:15493000-15510000	Weak transcription	Lung	lung
5	chr9:15493000-15510000	Weak transcription	Pancreas	Pancrea
6	chr9:15493000-15510000	Weak transcription	Spleen	Spleen
7	chr9:15493400-15510000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:15494000-15510000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:15500400-15510000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:15501000-15510000	Weak transcription	Stomach Mucosa	stomach
11	chr9:15507400-15510000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:15507600-15510200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
13	chr9:15507800-15510000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
14	chr9:15507800-15510000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
15	chr9:15508000-15510000	Weak transcription	Left Ventricle	heart
16	chr9:15508200-15510000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
17	chr9:15508200-15510200	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr9:15508200-15511800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr9:15508400-15511400	Active TSS	Brain Cingulate Gyrus	brain
20	chr9:15508600-15513200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr9:15508800-15510000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:15508800-15510000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr9:15508800-15510000	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr9:15508800-15510000	Flanking Active TSS	Fetal Lung	lung
25	chr9:15508800-15511400	Active TSS	Brain Angular Gyrus	brain
26	chr9:15508800-15511800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:15509000-15510200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:15509000-15510200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr9:15509000-15511400	Active TSS	GM12878-XiMat	blood
30	chr9:15509000-15511600	Active TSS	Right Atrium	heart
31	chr9:15509000-15511800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr9:15509200-15510000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr9:15509200-15510000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr9:15509200-15510000	Flanking Active TSS	HepG2	liver
35	chr9:15509200-15510000	Flanking Active TSS	HUVEC	blood vessel
36	chr9:15509200-15510000	Flanking Active TSS	NHDF-Ad	bronchial
37	chr9:15509200-15510200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr9:15509200-15510200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr9:15509200-15510200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr9:15509200-15510200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:15509200-15510200	Active TSS	Fetal Brain Male	brain
42	chr9:15509200-15511600	Active TSS	K562	blood
43	chr9:15509200-15511800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:15509200-15511800	Active TSS	Stomach Smooth Muscle	stomach
45	chr9:15509200-15511800	Active TSS	NHLF	lung
46	chr9:15509400-15510000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:15509400-15510000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr9:15509400-15510000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:15509400-15510000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr9:15509400-15510000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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