Variant report

Variant	rs62571018
Chromosome Location	chr9:15511799-15511800
allele	G/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	HCFC1	chr9:15509880-15511907	Hela-S3	cervix:	n/a	n/a
2	PML	chr9:15509949-15511805	GM12878	blood:	n/a	chr9:15511241-15511249
3	POLR2A	chr9:15509777-15511886	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr9:15510242-15511803	A549	lung:	n/a	chr9:15510778-15510788 chr9:15511615-15511624 chr9:15511443-15511452
5	MXI1	chr9:15509953-15511896	GM12878	blood:	n/a	n/a
6	JUND	chr9:15510391-15511914	SK-N-SH	brain:	n/a	chr9:15510781-15510790 chr9:15510567-15510581 chr9:15510782-15510791
7	CHD1	chr9:15509339-15512413	IMR90	lung:	n/a	chr9:15510554-15510564 chr9:15510784-15510794 chr9:15510444-15510454 chr9:15511226-15511236
8	SREBP1	chr9:15510259-15513935	GM12878	blood:	n/a	n/a
9	REST	chr9:15509584-15511948	H1-neurons	neurons:	n/a	chr9:15511508-15511521 chr9:15511043-15511053
10	CHD1	chr9:15509050-15513782	H1-hESC	embryonic stem cell:	n/a	chr9:15510554-15510564 chr9:15510784-15510794 chr9:15510444-15510454 chr9:15511226-15511236
11	CHD1	chr9:15508987-15513035	GM12878	blood:	n/a	chr9:15510554-15510564 chr9:15510784-15510794 chr9:15510444-15510454 chr9:15511226-15511236
12	POLR2A	chr9:15509843-15511854	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:15421340..15424109-chr9:15510012..15511838,2	K562	blood:
2	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:
3	chr9:15511224..15513667-chr9:15516724..15518268,2	K562	blood:
4	chr9:15510875..15512396-chr9:15551516..15553319,2	MCF-7	breast:

Variant related genes	Relation type
PSIP1	TF binding region
ENSG00000164975	Chromatin interaction
ENSG00000164989	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs16933296	0.90[EUR][1000 genomes]
rs16933350	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3087653	0.95[EUR][1000 genomes]
rs41268961	0.95[EUR][1000 genomes]
rs41306098	0.95[EUR][1000 genomes]
rs56361298	0.80[EUR][1000 genomes]
rs57191285	0.80[EUR][1000 genomes]
rs57467578	0.80[EUR][1000 genomes]
rs57849124	0.80[EUR][1000 genomes]
rs59355275	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59520337	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570969	0.81[EUR][1000 genomes]
rs62570970	0.85[EUR][1000 genomes]
rs62570971	0.85[EUR][1000 genomes]
rs62570972	0.81[EUR][1000 genomes]
rs62570973	0.85[EUR][1000 genomes]
rs62570974	0.85[EUR][1000 genomes]
rs62570975	0.85[EUR][1000 genomes]
rs62570976	0.90[EUR][1000 genomes]
rs62570980	0.95[EUR][1000 genomes]
rs62570991	0.95[EUR][1000 genomes]
rs62570992	0.95[EUR][1000 genomes]
rs62570993	0.95[EUR][1000 genomes]
rs62571001	0.90[EUR][1000 genomes]
rs62571002	0.90[EUR][1000 genomes]
rs62571003	0.92[EUR][1000 genomes]
rs62571007	0.95[EUR][1000 genomes]
rs62571008	0.92[EUR][1000 genomes]
rs62571009	0.95[EUR][1000 genomes]
rs62571011	0.95[EUR][1000 genomes]
rs62571015	0.95[EUR][1000 genomes]
rs62571016	0.95[EUR][1000 genomes]
rs62571017	0.95[EUR][1000 genomes]
rs62571021	0.80[EUR][1000 genomes]
rs62571022	0.80[EUR][1000 genomes]
rs62571023	0.80[EUR][1000 genomes]
rs62571024	0.80[EUR][1000 genomes]
rs62571027	0.80[EUR][1000 genomes]
rs62571029	1.00[EUR][1000 genomes]
rs62571033	0.95[EUR][1000 genomes]
rs62571037	0.92[EUR][1000 genomes]
rs62571046	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62571047	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62571048	0.90[EUR][1000 genomes]
rs62571050	0.87[EUR][1000 genomes]
rs62571051	0.85[EUR][1000 genomes]
rs62571052	0.82[EUR][1000 genomes]
rs73408328	0.80[EUR][1000 genomes]
rs73408340	0.80[EUR][1000 genomes]
rs7856523	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7856657	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7863139	0.80[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
rs62571018	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15508200-15511800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr9:15508600-15513200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr9:15508800-15511800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:15509000-15511800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr9:15509200-15511800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:15509200-15511800	Active TSS	Stomach Smooth Muscle	stomach
7	chr9:15509200-15511800	Active TSS	NHLF	lung
8	chr9:15509400-15511800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:15509400-15511800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr9:15509400-15512000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr9:15509600-15511800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:15509600-15511800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:15509600-15511800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:15509600-15511800	Active TSS	Aorta	Aorta
15	chr9:15509600-15511800	Active TSS	Brain Substantia Nigra	brain
16	chr9:15509600-15511800	Active TSS	Fetal Muscle Leg	muscle
17	chr9:15509600-15511800	Active TSS	Thymus	Thymus
18	chr9:15509600-15512000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:15509600-15512600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:15509800-15511800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:15510000-15511800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr9:15510000-15511800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr9:15510000-15511800	Active TSS	Fetal Heart	heart
24	chr9:15510000-15511800	Active TSS	Fetal Kidney	kidney
25	chr9:15510000-15511800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr9:15510000-15511800	Active TSS	Rectal Smooth Muscle	rectum
27	chr9:15510000-15511800	Active TSS	Right Ventricle	heart
28	chr9:15510000-15511800	Active TSS	HSMMtube	muscle
29	chr9:15510000-15511800	Active TSS	NHDF-Ad	bronchial
30	chr9:15510000-15512000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:15510000-15512400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr9:15510200-15511800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr9:15510200-15511800	Active TSS	HSMM	muscle
34	chr9:15511000-15511800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:15511000-15511800	Flanking Active TSS	Liver	Liver
36	chr9:15511000-15511800	Active TSS	Fetal Brain Male	brain
37	chr9:15511000-15511800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr9:15511200-15511800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr9:15511200-15511800	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr9:15511200-15511800	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr9:15511200-15511800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr9:15511200-15511800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr9:15511200-15511800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:15511200-15511800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr9:15511200-15511800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr9:15511400-15511800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr9:15511400-15511800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr9:15511400-15511800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr9:15511400-15511800	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr9:15511400-15511800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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