Variant report

Variant	rs62571015
Chromosome Location	chr9:15509198-15509199
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	chr9:15507256..15510187-chr9:15510704..15514473,5	K562	blood:

Variant related genes	Relation type
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 53 )
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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59520337	0.95[EUR][1000 genomes]
rs62570969	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570970	0.80[EUR][1000 genomes]
rs62570971	0.80[EUR][1000 genomes]
rs62570972	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570973	0.80[EUR][1000 genomes]
rs62570974	0.80[EUR][1000 genomes]
rs62570975	0.80[EUR][1000 genomes]
rs62570976	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62570980	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62570991	0.80[AFR][1000 genomes];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	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62571011	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62571016	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571017	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571018	0.95[EUR][1000 genomes]
rs62571029	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571031	0.81[EUR][1000 genomes]
rs62571032	0.81[EUR][1000 genomes]
rs62571033	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571037	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62571046	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571047	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62571048	0.90[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	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7856657	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7856710	0.81[EUR][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
rs62571015	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
3	chr9:15476600-15510000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:15477000-15509600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:15481600-15509600	Weak transcription	Aorta	Aorta
6	chr9:15485800-15509800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:15492600-15509800	Weak transcription	Colonic Mucosa	Colon
8	chr9:15493000-15509800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:15493000-15510000	Weak transcription	Gastric	stomach
10	chr9:15493000-15510000	Weak transcription	Lung	lung
11	chr9:15493000-15510000	Weak transcription	Pancreas	Pancrea
12	chr9:15493000-15510000	Weak transcription	Spleen	Spleen
13	chr9:15493200-15509600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:15493400-15510000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:15494000-15509200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:15494000-15510000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:15500400-15509800	Weak transcription	Psoas Muscle	Psoas
18	chr9:15500400-15510000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:15501000-15510000	Weak transcription	Stomach Mucosa	stomach
20	chr9:15505200-15509400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr9:15506400-15509400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr9:15506400-15509400	Weak transcription	Brain Substantia Nigra	brain
23	chr9:15506600-15509200	Weak transcription	NH-A	brain
24	chr9:15506600-15509400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:15506600-15509400	Weak transcription	HSMM	muscle
26	chr9:15506600-15509800	Weak transcription	Placenta	Placenta
27	chr9:15507000-15509400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:15507200-15509400	Weak transcription	Adipose Nuclei	Adipose
29	chr9:15507400-15509600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:15507400-15510000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:15507600-15509200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:15507600-15509600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:15507600-15509600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:15507600-15509600	Weak transcription	Liver	Liver
35	chr9:15507600-15510200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
36	chr9:15507800-15509400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:15507800-15509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:15507800-15509400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:15507800-15509800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
40	chr9:15507800-15509800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:15507800-15510000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
42	chr9:15507800-15510000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
43	chr9:15508000-15509200	Weak transcription	Osteobl	bone
44	chr9:15508000-15509400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:15508000-15510000	Weak transcription	Left Ventricle	heart
46	chr9:15508200-15509400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:15508200-15509600	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:15508200-15510000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
49	chr9:15508200-15510200	Transcr. at gene 5' and 3'	Dnd41	blood
50	chr9:15508200-15511800	Active TSS	Brain Inferior Temporal Lobe	brain

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