Variant report

Variant	rs62570991
Chromosome Location	chr9:15451501-15451502
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	chr9:15450513..15453468-chr9:15464401..15466619,2	K562	blood:

Extended variants
information (count: 47 )
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	0.83[AFR][1000 genomes];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	0.80[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62570980	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570992	0.93[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: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	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	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
rs62570991	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	chr9:15426400-15468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:15434000-15464000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:15438400-15469800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr9:15438800-15468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr9:15441800-15457000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:15442000-15458600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:15442000-15463000	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:15442200-15469400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr9:15442400-15451800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:15442400-15464400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr9:15442600-15455200	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr9:15442600-15455200	Strong transcription	Dnd41	blood
15	chr9:15442600-15478200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr9:15442600-15478600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr9:15442800-15453400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:15442800-15456200	Strong transcription	Fetal Muscle Leg	muscle
19	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
20	chr9:15443000-15455400	Strong transcription	Adipose Nuclei	Adipose
21	chr9:15443000-15457000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr9:15443000-15462400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:15443000-15463800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr9:15443000-15470200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr9:15443000-15478000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr9:15443000-15482200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:15443200-15455200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:15443200-15455400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr9:15443200-15456600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:15443200-15456600	Strong transcription	Placenta	Placenta
31	chr9:15443200-15460000	Strong transcription	NH-A	brain
32	chr9:15443200-15460600	Strong transcription	Primary B cells from cord blood	blood
33	chr9:15443200-15465600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:15443200-15469200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:15443200-15478000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr9:15443200-15479600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:15443400-15455400	Strong transcription	Colon Smooth Muscle	Colon
40	chr9:15443400-15455800	Strong transcription	HepG2	liver
41	chr9:15443400-15456800	Strong transcription	GM12878-XiMat	blood
42	chr9:15443400-15466400	Strong transcription	HSMM	muscle
43	chr9:15443400-15467400	Strong transcription	Fetal Brain Female	brain
44	chr9:15443400-15469000	Strong transcription	Osteobl	bone
45	chr9:15443400-15469600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:15443400-15469600	Strong transcription	Fetal Intestine Large	intestine
47	chr9:15443400-15479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr9:15443600-15452000	Strong transcription	Brain Hippocampus Middle	brain
49	chr9:15443600-15453000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr9:15443600-15454400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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