Variant report

Variant	rs62570975
Chromosome Location	chr9:15432441-15432442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:15422069..15423659-chr9:15430578..15433740,3	K562	blood:
2	chr9:15420595..15424773-chr9:15424796..15433036,11	MCF-7	breast:
3	chr9:15422138..15423750-chr9:15430824..15433204,2	K562	blood:

Variant related genes	Relation type
ENSG00000164975	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10962016	0.81[EUR][1000 genomes]
rs16933296	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16933350	0.85[EUR][1000 genomes]
rs3087653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41268961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41306098	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59355275	0.80[EUR][1000 genomes]
rs59520337	0.85[EUR][1000 genomes]
rs62570966	0.88[EUR][1000 genomes]
rs62570967	0.88[EUR][1000 genomes]
rs62570969	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570970	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570972	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62570976	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570980	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570991	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570992	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62570993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62571001	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62571002	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62571003	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62571007	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62571008	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62571009	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62571011	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62571015	0.80[EUR][1000 genomes]
rs62571016	0.80[EUR][1000 genomes]
rs62571017	0.80[EUR][1000 genomes]
rs62571018	0.85[EUR][1000 genomes]
rs62571029	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62571033	0.80[EUR][1000 genomes]
rs62573013	0.88[EUR][1000 genomes]
rs62573015	0.88[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
rs62570975	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	chr9:15424000-15443400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:15424000-15443600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:15425000-15437000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:15425400-15433600	Weak transcription	Fetal Kidney	kidney
7	chr9:15425400-15439000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:15425800-15433800	Weak transcription	HSMMtube	muscle
9	chr9:15425800-15434000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:15426200-15441800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:15426400-15433000	Weak transcription	NHLF	lung
12	chr9:15426400-15433600	Weak transcription	Primary T cells from cord blood	blood
13	chr9:15426400-15433600	Weak transcription	Thymus	Thymus
14	chr9:15426400-15434000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:15426400-15435400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:15426400-15436000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:15426400-15439000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:15426400-15439800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:15426400-15441800	Weak transcription	Spleen	Spleen
20	chr9:15426400-15442800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:15426400-15443600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:15426400-15443600	Weak transcription	Gastric	stomach
23	chr9:15426400-15468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:15426600-15433600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:15426600-15433600	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:15426600-15433600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:15426600-15434000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:15426600-15434000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr9:15426600-15442400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:15426600-15443400	Weak transcription	Fetal Heart	heart
31	chr9:15426800-15433000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:15426800-15433000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:15426800-15433200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:15426800-15433200	Weak transcription	NHDF-Ad	bronchial
35	chr9:15426800-15433400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:15426800-15433600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:15426800-15433600	Weak transcription	HMEC	breast
38	chr9:15426800-15433600	Weak transcription	Osteobl	bone
39	chr9:15426800-15434200	Weak transcription	Fetal Brain Male	brain
40	chr9:15427000-15433600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:15427000-15433800	Weak transcription	Fetal Lung	lung
42	chr9:15427000-15436000	Weak transcription	Fetal Brain Female	brain
43	chr9:15427000-15443400	Weak transcription	NHEK	skin
44	chr9:15427800-15433600	Weak transcription	Placenta	Placenta
45	chr9:15428000-15432600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr9:15428400-15433600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:15429400-15433000	Weak transcription	Dnd41	blood
48	chr9:15429400-15433800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr9:15429800-15432600	Weak transcription	HSMM	muscle
50	chr9:15430000-15433400	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links