Variant report

Variant	rs517533
Chromosome Location	chr1:120229170-120229171
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	chr1:120228899..120230823-chr1:120252883..120254482,3	K562	blood:
2	chr1:120201468..120203936-chr1:120227874..120229485,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1163251	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2764886	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs477992	0.89[ASN][1000 genomes]
rs478093	0.85[ASN][1000 genomes]
rs478450	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs483180	0.83[ASN][1000 genomes]
rs483360	0.85[EUR][1000 genomes]
rs487081	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487884	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs496195	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs496198	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511059	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs514491	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs532303	0.87[ASN][1000 genomes]
rs539708	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs541503	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs561931	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs592762	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs594400	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs595283	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs597308	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs598685	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs606312	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612430	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627707	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs629735	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639216	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639761	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640195	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658442	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs660073	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662243	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662602	0.83[ASN][1000 genomes]
rs677277	0.86[EUR][1000 genomes]
rs839600	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs839605	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839608	0.88[EUR][1000 genomes]
rs866321	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120222800-120231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:120225800-120229400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:120227000-120231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:120228200-120232200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:120228400-120229600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr1:120228400-120230000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:120228400-120232400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:120228600-120229200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:120228600-120229800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:120228600-120233000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:120228800-120230200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:120229000-120229200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:120229000-120229200	Flanking Active TSS	NHEK	skin
14	chr1:120229000-120229400	Flanking Active TSS	HMEC	breast
15	chr1:120229000-120229600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:120229000-120229600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:120229000-120230200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:120229000-120230200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:120229000-120230400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:120229000-120230400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr1:120229000-120230400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:120229000-120230600	Enhancers	Placenta	Placenta
23	chr1:120229000-120230800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:120229000-120230800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:120229000-120232200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:120229000-120232400	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links