Variant report

Variant	rs62570980
Chromosome Location	chr9:15443039-15443040
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	PAX5	chr9:15442862-15443235	GM12878	blood:	n/a	n/a
2	PAX5	chr9:15442817-15443272	GM12878	blood:	n/a	n/a
3	PAX5	chr9:15442953-15443145	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SNAPC3	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs16933296	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16933350	0.95[EUR][1000 genomes]
rs3087653	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41268961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41306098	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55649599	0.84[EUR][1000 genomes]
rs59355275	0.90[EUR][1000 genomes]
rs59520337	0.95[EUR][1000 genomes]
rs62570969	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62570970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570971	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570972	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62570973	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570974	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570975	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62570991	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570992	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570993	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571001	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571002	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571003	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62571007	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571008	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62571009	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571011	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571015	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62571016	0.90[EUR][1000 genomes]
rs62571017	0.90[EUR][1000 genomes]
rs62571018	0.95[EUR][1000 genomes]
rs62571029	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571033	0.90[EUR][1000 genomes]
rs62571037	0.87[EUR][1000 genomes]
rs62571046	0.85[EUR][1000 genomes]
rs62571047	0.85[EUR][1000 genomes]
rs62571048	0.85[EUR][1000 genomes]
rs62571050	0.83[EUR][1000 genomes]
rs62571051	0.80[EUR][1000 genomes]
rs7856523	0.85[EUR][1000 genomes]
rs7856657	0.83[EUR][1000 genomes]
rs7863139	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv831520	chr9:15404866-15444447	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	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
rs62570980	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	chr9:15424000-15443400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:15424000-15443600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:15426400-15443600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:15426400-15443600	Weak transcription	Gastric	stomach
5	chr9:15426400-15468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:15426600-15443400	Weak transcription	Fetal Heart	heart
7	chr9:15427000-15443400	Weak transcription	NHEK	skin
8	chr9:15431400-15443400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:15431400-15443400	Weak transcription	Pancreas	Pancrea
10	chr9:15431400-15443600	Weak transcription	Aorta	Aorta
11	chr9:15431400-15443600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:15431400-15443600	Weak transcription	Esophagus	oesophagus
13	chr9:15431400-15445800	Weak transcription	Right Ventricle	heart
14	chr9:15431400-15446000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:15431400-15447800	Weak transcription	Psoas Muscle	Psoas
16	chr9:15431600-15443400	Weak transcription	Stomach Mucosa	stomach
17	chr9:15432200-15443600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:15434000-15464000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:15434400-15443400	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:15434400-15443600	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:15434400-15443600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:15434400-15443600	Weak transcription	K562	blood
24	chr9:15434400-15443800	Weak transcription	HSMMtube	muscle
25	chr9:15434800-15443600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:15434800-15443600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:15435000-15443200	Weak transcription	Brain Anterior Caudate	brain
28	chr9:15435000-15443400	Weak transcription	Fetal Brain Male	brain
29	chr9:15435000-15443400	Weak transcription	Ovary	ovary
30	chr9:15435000-15443600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:15435000-15443600	Weak transcription	Left Ventricle	heart
32	chr9:15435000-15444400	Weak transcription	Brain Substantia Nigra	brain
33	chr9:15435200-15443200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr9:15435200-15443200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:15435200-15443200	Weak transcription	Colonic Mucosa	Colon
36	chr9:15435200-15443200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:15435200-15443400	Weak transcription	NHLF	lung
38	chr9:15435200-15443600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:15435200-15443600	Weak transcription	HMEC	breast
40	chr9:15435200-15443600	Weak transcription	NHDF-Ad	bronchial
41	chr9:15435400-15443200	Weak transcription	NH-A	brain
42	chr9:15435400-15443600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:15435400-15443800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:15436400-15443400	Weak transcription	HUVEC	blood vessel
45	chr9:15436600-15443200	Weak transcription	Placenta	Placenta
46	chr9:15436600-15443600	Weak transcription	A549	lung
47	chr9:15438000-15446400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:15438400-15447800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr9:15438400-15469800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr9:15438600-15444200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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