Variant report

Variant	rs6478109
Chromosome Location	chr9:117568766-117568767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr9:117568575-117568841	GM12878	blood:	n/a	n/a
2	IKZF1	chr9:117568418-117568925	GM12878	blood:	n/a	n/a
3	POU2F2	chr9:117568629-117568887	GM12878	blood:	n/a	chr9:117568660-117568671 chr9:117568785-117568792
4	POLR2A	chr9:117568047-117568845	MCF10A-Er-Src	breast:	n/a	n/a
5	RUNX3	chr9:117568480-117568954	GM12878	blood:	n/a	n/a
6	TEAD4	chr9:117567796-117568859	ECC-1	luminal epithelium:	n/a	n/a
7	RELA	chr9:117568514-117568895	GM12878	blood:	n/a	chr9:117568607-117568616 chr9:117568607-117568616
8	STAT3	chr9:117568527-117568783	MCF10A-Er-Src	breast:	n/a	chr9:117568727-117568738
9	WRNIP1	chr9:117568712-117568792	GM12878	blood:	n/a	n/a
10	RUNX3	chr9:117568523-117568953	GM12878	blood:	n/a	n/a
11	TCF12	chr9:117567789-117568869	A549	lung:	n/a	chr9:117568296-117568306
12	STAT3	chr9:117568621-117568783	MCF10A-Er-Src	breast:	n/a	chr9:117568727-117568738
13	FOS	chr9:117568604-117568766	MCF10A-Er-Src	breast:	n/a	n/a
14	TCF3	chr9:117568602-117568843	GM12878	blood:	n/a	n/a
15	MAX	chr9:117567796-117568802	ECC-1	luminal epithelium:	n/a	chr9:117568787-117568796
16	RELA	chr9:117568438-117569101	GM19099	blood:	n/a	chr9:117568607-117568616 chr9:117568607-117568616
17	STAT3	chr9:117568641-117568856	MCF10A-Er-Src	breast:	n/a	chr9:117568727-117568738
18	TCF3	chr9:117568506-117568893	GM12878	blood:	n/a	n/a
19	MYC	chr9:117567847-117568892	MCF10A-Er-Src	breast:	n/a	chr9:117568787-117568796
20	EBF1	chr9:117568550-117568827	GM12878	blood:	n/a	n/a
21	PRDM1	chr9:117568641-117568883	Hela-S3	cervix:	n/a	chr9:117568730-117568739 chr9:117568726-117568740 chr9:117568725-117568740 chr9:117568726-117568739
22	SPI1	chr9:117568557-117568871	GM12891	blood:	n/a	chr9:117568727-117568736

Variant related genes	Relation type
TNFSF15	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10114470	0.92[AFR][1000 genomes]
rs10817678	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810936	0.88[ASW][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.92[AFR][1000 genomes]
rs4246905	0.84[MEX][hapmap]
rs4263839	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4366152	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4372078	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6478108	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7848647	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Inflammatory bowel disease	18758464	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6478109	DNAJC25	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117565000-117569400	Enhancers	Fetal Lung	lung
2	chr9:117565200-117569800	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr9:117565800-117568800	Enhancers	NHLF	lung
4	chr9:117565800-117569000	Enhancers	HepG2	liver
5	chr9:117566000-117569000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:117566200-117568800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:117566200-117569000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:117566200-117569600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:117566400-117569000	Enhancers	HSMM	muscle
10	chr9:117566400-117569200	Enhancers	NH-A	brain
11	chr9:117566600-117569000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:117566800-117569200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr9:117567400-117568800	Flanking Active TSS	NHEK	skin
14	chr9:117567600-117569200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr9:117567800-117568800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:117567800-117568800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:117567800-117569000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr9:117567800-117569000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr9:117567800-117569000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr9:117567800-117569000	Enhancers	Dnd41	blood
21	chr9:117567800-117569400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr9:117567800-117572000	Enhancers	Primary B cells from peripheral blood	blood
23	chr9:117568000-117568800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr9:117568000-117568800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:117568000-117568800	Enhancers	H9 Cell Line	embryonic stem cell
26	chr9:117568000-117568800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:117568000-117568800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:117568000-117568800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr9:117568000-117568800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr9:117568000-117568800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:117568000-117568800	Active TSS	Rectal Smooth Muscle	rectum
32	chr9:117568000-117569000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr9:117568000-117569000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:117568000-117569000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr9:117568000-117569000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr9:117568000-117569000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:117568000-117569000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr9:117568000-117569000	Enhancers	Small Intestine	intestine
39	chr9:117568000-117569000	Flanking Active TSS	HMEC	breast
40	chr9:117568000-117569200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:117568000-117569200	Enhancers	Primary T cells from cord blood	blood
42	chr9:117568000-117569200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr9:117568000-117569400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr9:117568000-117569400	Enhancers	Fetal Thymus	thymus
45	chr9:117568000-117569400	Enhancers	Thymus	Thymus
46	chr9:117568000-117569600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr9:117568000-117569600	Enhancers	Fetal Muscle Leg	muscle
48	chr9:117568000-117569800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr9:117568000-117569800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr9:117568000-117569800	Enhancers	Primary T helper cells fromperipheralblood	blood

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