Variant report

Variant	rs6696825
Chromosome Location	chr1:209982372-209982373
allele	A/G
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:9)
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: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	chr1:209970799..209973393-chr1:209981570..209983608,2	K562	blood:
8	chr1:209982154..209983681-chr1:210545810..210547417,2	K562	blood:
9	chr1:209979780..209981458-chr1:209981509..209984915,3	K562	blood:

No data

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

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1044516	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes]
rs11803382	0.87[EUR][1000 genomes]
rs11805830	0.87[EUR][1000 genomes]
rs12070337	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1415543	0.82[TSI][hapmap]
rs17015183	0.84[EUR][1000 genomes]
rs17015218	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs17015224	0.87[EUR][1000 genomes]
rs17015226	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs17015259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015309	0.87[TSI][hapmap]
rs17317411	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2073485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235373	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753518	0.87[EUR][1000 genomes]
rs41305104	0.81[EUR][1000 genomes]
rs4556361	0.82[TSI][hapmap]
rs4844895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58637469	0.87[EUR][1000 genomes]
rs6540559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540560	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6540561	0.87[EUR][1000 genomes]
rs6694552	0.87[EUR][1000 genomes]
rs742214	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522250	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525951	0.86[TSI][hapmap]
rs7550857	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs764093	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926346	0.87[EUR][1000 genomes]
rs926347	0.86[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6696825	SYT14	cis	parietal	SCAN
rs6696825	LPGAT1	cis	cerebellum	SCAN
rs6696825	TRAF3IP3	cis	Whole Blood	GTEx
rs6696825	G0S2	cis	parietal	SCAN
rs6696825	IRF6	cis	cerebellum	SCAN

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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