Variant report

Variant	rs62570969
Chromosome Location	chr9:15425700-15425701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15420595..15424773-chr9:15424796..15433036,11	MCF-7	breast:
2	chr9:15420090..15425077-chr9:15425243..15430966,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164975	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10962016	0.86[EUR][1000 genomes]
rs16933296	0.91[AMR][1000 genomes]
rs16933350	0.81[EUR][1000 genomes]
rs3087653	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41268961	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41306098	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59355275	0.85[EUR][1000 genomes]
rs59520337	0.81[EUR][1000 genomes]
rs62570966	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62570967	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62570970	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570971	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570972	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570973	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570974	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570975	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570976	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62570980	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62570991	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62570992	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62570993	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62571001	0.91[AMR][1000 genomes]
rs62571002	0.91[AMR][1000 genomes]
rs62571007	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62571008	0.91[AMR][1000 genomes]
rs62571009	0.81[EUR][1000 genomes]
rs62571011	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62571015	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62571016	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62571017	0.85[EUR][1000 genomes]
rs62571018	0.81[EUR][1000 genomes]
rs62571029	0.81[EUR][1000 genomes]
rs62571033	0.85[EUR][1000 genomes]
rs62571037	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62571046	0.81[EUR][1000 genomes]
rs62571047	0.81[EUR][1000 genomes]
rs62571048	0.81[EUR][1000 genomes]
rs62573013	0.93[EUR][1000 genomes]
rs62573015	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7856523	0.81[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
rs62570969	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15423600-15434400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:15423600-15439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:15424000-15427600	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr9:15424000-15430200	Weak transcription	Small Intestine	intestine
5	chr9:15424000-15431000	Weak transcription	Psoas Muscle	Psoas
6	chr9:15424000-15443400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:15424000-15443600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:15424200-15425800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:15424200-15425800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:15424200-15426000	Weak transcription	Right Atrium	heart
11	chr9:15424200-15426600	Enhancers	Fetal Heart	heart
12	chr9:15424200-15426600	Strong transcription	Fetal Muscle Leg	muscle
13	chr9:15424200-15426800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:15424400-15426600	Genic enhancers	Dnd41	blood
15	chr9:15424600-15425800	Genic enhancers	HUVEC	blood vessel
16	chr9:15424600-15426000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:15424600-15426000	Genic enhancers	Monocytes-CD14+_RO01746	blood
18	chr9:15424600-15426400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:15424600-15426600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:15424600-15426800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr9:15424600-15427000	Genic enhancers	Fetal Lung	lung
22	chr9:15424600-15427800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr9:15424600-15428400	Strong transcription	Fetal Thymus	thymus
24	chr9:15424600-15430400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:15424800-15425800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:15424800-15425800	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:15424800-15426000	Strong transcription	Colonic Mucosa	Colon
28	chr9:15424800-15426200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr9:15424800-15426400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:15424800-15426400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:15424800-15426400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:15424800-15426400	Genic enhancers	Primary B cells from cord blood	blood
33	chr9:15424800-15426400	Strong transcription	Primary T cells from cord blood	blood
34	chr9:15424800-15426400	Strong transcription	Brain Cingulate Gyrus	brain
35	chr9:15424800-15426400	Genic enhancers	Left Ventricle	heart
36	chr9:15424800-15426600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr9:15424800-15426600	Genic enhancers	Brain Hippocampus Middle	brain
38	chr9:15424800-15426600	Strong transcription	Brain Substantia Nigra	brain
39	chr9:15424800-15426600	Genic enhancers	Colon Smooth Muscle	Colon
40	chr9:15424800-15426600	Genic enhancers	Duodenum Mucosa	Duodenum
41	chr9:15424800-15426600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
42	chr9:15424800-15426600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr9:15424800-15426600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr9:15424800-15426800	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr9:15424800-15427000	Genic enhancers	HepG2	liver
46	chr9:15424800-15427400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:15424800-15427400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr9:15424800-15427800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
49	chr9:15424800-15427800	Strong transcription	Placenta	Placenta
50	chr9:15424800-15428000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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