Variant report

Variant	rs6540561
Chromosome Location	chr1:209982255-209982256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:209982102-209982463	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209979052..209983681-chr1:210545344..210549112,5	K562	blood:
2	chr1:209981459..209983151-chr1:209995817..209998034,2	MCF-7	breast:
3	chr1:209981422..209983543-chr1:209995395..209998153,2	K562	blood:
4	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
5	chr1:209980787..209983095-chr1:209985152..209988028,2	K562	blood:
6	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
7	chr1:209968649..209970778-chr1:209979506..209982286,2	K562	blood:
8	chr1:209970799..209973393-chr1:209981570..209983608,2	K562	blood:
9	chr1:209982154..209983681-chr1:210545810..210547417,2	K562	blood:
10	chr1:209979780..209981458-chr1:209981509..209984915,3	K562	blood:

No data

Variant related genes	Relation type
IRF6	TF binding region
ENSG00000200972	Chromatin interaction
ENSG00000117597	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1044516	0.86[EUR][1000 genomes]
rs1073150	0.86[ASN][1000 genomes]
rs11803382	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070337	0.90[AFR][1000 genomes]
rs1415543	0.86[ASN][1000 genomes]
rs17015183	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17015218	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17015224	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17015226	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17015259	0.87[EUR][1000 genomes]
rs17015309	0.93[ASN][1000 genomes]
rs17015330	0.93[ASN][1000 genomes]
rs17015361	0.86[ASN][1000 genomes]
rs17015379	0.83[ASN][1000 genomes]
rs17317411	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17389436	0.81[AMR][1000 genomes]
rs2073485	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2235372	0.87[EUR][1000 genomes]
rs2235373	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2357230	0.90[ASN][1000 genomes]
rs35508116	0.81[ASN][1000 genomes]
rs3753518	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41305104	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4556361	0.90[ASN][1000 genomes]
rs4844895	0.87[EUR][1000 genomes]
rs58637469	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59100111	0.90[ASN][1000 genomes]
rs61747285	0.93[ASN][1000 genomes]
rs6540559	0.87[EUR][1000 genomes]
rs6540560	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540563	0.90[ASN][1000 genomes]
rs6540564	0.90[ASN][1000 genomes]
rs6694552	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696825	0.87[EUR][1000 genomes]
rs6698154	0.93[ASN][1000 genomes]
rs73093853	0.86[ASN][1000 genomes]
rs742214	0.87[EUR][1000 genomes]
rs742215	0.87[EUR][1000 genomes]
rs7511996	0.86[ASN][1000 genomes]
rs7522045	0.90[ASN][1000 genomes]
rs7522250	0.87[EUR][1000 genomes]
rs7525951	0.86[ASN][1000 genomes]
rs7539638	0.88[ASN][1000 genomes]
rs7550857	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs764093	0.87[EUR][1000 genomes]
rs926346	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926347	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6540561	TRAF3IP3	cis	Whole Blood	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209979600-209985000	Weak transcription	Gastric	stomach
2	chr1:209979800-209989200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209980000-209982400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:209980000-209982600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:209980000-209983600	Enhancers	Fetal Intestine Large	intestine
6	chr1:209980000-209983600	Enhancers	Fetal Intestine Small	intestine
7	chr1:209980200-209982400	Enhancers	K562	blood
8	chr1:209980800-209984400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:209980800-209985600	Enhancers	HMEC	breast
10	chr1:209981000-209982400	Enhancers	Placenta	Placenta
11	chr1:209981000-209985800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:209981200-209984400	Enhancers	NHEK	skin
13	chr1:209981600-209984200	Enhancers	Fetal Thymus	thymus
14	chr1:209981800-209982400	Enhancers	Fetal Heart	heart
15	chr1:209981800-209984600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:209981800-209989200	Weak transcription	Esophagus	oesophagus
17	chr1:209981800-209989600	Weak transcription	Spleen	Spleen
18	chr1:209981800-209989800	Weak transcription	Right Atrium	heart
19	chr1:209982000-209983400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:209982000-209989200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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