Variant report

Variant	rs6540560
Chromosome Location	chr1:209982073-209982074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:209982040-209982190	SH-SY5Y	brain:	n/a	n/a
2	RFX5	chr1:209982043-209982182	HepG2	liver:	n/a	n/a
3	RFX5	chr1:209982035-209982205	GM12878	blood:	n/a	n/a
4	RCOR1	chr1:209981137-209982147	IMR90	lung:	n/a	n/a
5	JUN	chr1:209981252-209982200	K562	blood:	n/a	chr1:209981572-209981583
6	EP300	chr1:209981184-209982078	SK-N-SH	brain:	n/a	n/a

No data

(count:9 , 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	chr1:209979780..209981458-chr1:209981509..209984915,3	K562	blood:

No data

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

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1005287	0.83[AFR][1000 genomes]
rs1044516	0.86[ASW][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1073150	0.86[ASN][1000 genomes]
rs11803382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070337	0.94[AFR][1000 genomes]
rs12403599	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs1319072	0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1415543	0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs17015183	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17015218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17015224	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17015226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[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	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.93[ASN][1000 genomes]
rs17015330	0.93[ASN][1000 genomes]
rs17015361	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17015379	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs17317411	1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17389436	0.81[AMR][1000 genomes]
rs2013162	0.95[YRI][hapmap]
rs2073485	0.93[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2073486	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs2073487	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs2235372	0.86[ASW][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2235373	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2235375	0.95[YRI][hapmap]
rs2236908	0.95[YRI][hapmap]
rs2236909	0.95[YRI][hapmap]
rs2357229	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs2357230	0.90[ASN][1000 genomes]
rs35508116	0.81[ASN][1000 genomes]
rs3753518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[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	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs4844895	0.86[ASW][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs58637469	0.96[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]
rs6540561	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540563	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6540564	0.90[ASN][1000 genomes]
rs6659549	0.83[AFR][1000 genomes]
rs6685182	0.95[YRI][hapmap]
rs6694552	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696825	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6698154	0.93[ASN][1000 genomes]
rs73093853	0.86[ASN][1000 genomes]
rs742214	0.87[EUR][1000 genomes]
rs742215	1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7511996	0.86[ASN][1000 genomes]
rs7522045	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7522250	0.87[EUR][1000 genomes]
rs7525951	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs7539638	0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7545538	0.82[AFR][1000 genomes]
rs7545542	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs7550857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552506	0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs764093	0.87[EUR][1000 genomes]
rs926346	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926347	0.96[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
rs6540560	TRAF3IP3	cis	Whole Blood	GTEx

Chromatin state (count:32 , 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	chr1:209980000-209982200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:209980000-209982200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:209980000-209982200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:209980000-209982200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:209980000-209982200	Enhancers	Stomach Mucosa	stomach
8	chr1:209980000-209982400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:209980000-209982600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:209980000-209983600	Enhancers	Fetal Intestine Large	intestine
11	chr1:209980000-209983600	Enhancers	Fetal Intestine Small	intestine
12	chr1:209980200-209982200	Enhancers	HUVEC	blood vessel
13	chr1:209980200-209982400	Enhancers	K562	blood
14	chr1:209980600-209982200	Enhancers	NHLF	lung
15	chr1:209980600-209982200	Enhancers	Osteobl	bone
16	chr1:209980800-209984400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:209980800-209985600	Enhancers	HMEC	breast
18	chr1:209981000-209982200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:209981000-209982200	Enhancers	NHDF-Ad	bronchial
20	chr1:209981000-209982400	Enhancers	Placenta	Placenta
21	chr1:209981000-209985800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:209981200-209984400	Enhancers	NHEK	skin
23	chr1:209981600-209984200	Enhancers	Fetal Thymus	thymus
24	chr1:209981800-209982200	Enhancers	HSMMtube	muscle
25	chr1:209981800-209982400	Enhancers	Fetal Heart	heart
26	chr1:209981800-209984600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:209981800-209989200	Weak transcription	Esophagus	oesophagus
28	chr1:209981800-209989600	Weak transcription	Spleen	Spleen
29	chr1:209981800-209989800	Weak transcription	Right Atrium	heart
30	chr1:209982000-209982200	Enhancers	Right Ventricle	heart
31	chr1:209982000-209983400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:209982000-209989200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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