Variant report

Variant	rs10757225
Chromosome Location	chr9:21555445-21555446
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:162350928..162351858-chr9:21554668..21555569,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000239887	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10118880	0.89[EUR][1000 genomes]
rs1013241	0.81[AMR][1000 genomes]
rs10738594	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965064	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1545749	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1983811	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4141712	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141713	0.92[EUR][1000 genomes]
rs7033598	0.82[AMR][1000 genomes]
rs9298816	0.92[EUR][1000 genomes]
rs9298817	0.82[EUR][1000 genomes]
rs9657572	0.97[EUR][1000 genomes]
rs9657607	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs996442	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
2	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10757225	LOC554202	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21545600-21555600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:21548400-21558200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:21552600-21558600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:21552800-21555800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:21552800-21556000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:21553000-21555600	Weak transcription	NHDF-Ad	bronchial
7	chr9:21553000-21555800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:21553000-21556000	Weak transcription	HSMM	muscle
9	chr9:21553000-21558600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:21553200-21555600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:21553600-21558000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:21553800-21555600	Weak transcription	Stomach Mucosa	stomach
13	chr9:21553800-21556000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:21553800-21556800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr9:21553800-21557400	Active TSS	A549	lung
16	chr9:21554200-21555800	Weak transcription	Fetal Intestine Large	intestine
17	chr9:21554200-21556800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:21554600-21556200	Transcr. at gene 5' and 3'	HMEC	breast
19	chr9:21554800-21558800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:21554800-21560600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr9:21555000-21555600	Active TSS	NHLF	lung
22	chr9:21555000-21555800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:21555000-21557400	Flanking Active TSS	HUVEC	blood vessel
24	chr9:21555000-21558600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:21555200-21555600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:21555200-21555800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:21555200-21555800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
28	chr9:21555200-21556200	Flanking Active TSS	Osteobl	bone
29	chr9:21555200-21556400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr9:21555200-21558600	Active TSS	Fetal Intestine Small	intestine
31	chr9:21555200-21560000	Active TSS	Hela-S3	cervix
32	chr9:21555200-21560800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:21555400-21555600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr9:21555400-21555600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
35	chr9:21555400-21555600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr9:21555400-21556200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:21555400-21556200	Transcr. at gene 5' and 3'	NH-A	brain
38	chr9:21555400-21556400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr9:21555400-21556400	Transcr. at gene 5' and 3'	NHEK	skin
40	chr9:21555400-21558600	Active TSS	Duodenum Mucosa	Duodenum

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