Variant report

Variant	rs7252417
Chromosome Location	chr19:39468640-39468641
allele	G/T
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	BHLHE40	chr19:39468558-39468975	GM12878	blood:	n/a	n/a
2	RUNX3	chr19:39468267-39469185	GM12878	blood:	n/a	n/a
3	BCL11A	chr19:39468513-39468871	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39468327-39468984	GM12892	blood:	n/a	n/a
5	BATF	chr19:39468143-39468965	GM12878	blood:	n/a	n/a
6	BCLAF1	chr19:39468331-39469110	GM12878	blood:	n/a	n/a
7	RELA	chr19:39468536-39468975	GM19193	blood:	n/a	n/a
8	TCF3	chr19:39468481-39468824	GM12878	blood:	n/a	n/a
9	TCF12	chr19:39468426-39468835	GM12878	blood:	n/a	n/a
10	PAX5	chr19:39468621-39468933	GM12878	blood:	n/a	chr19:39468868-39468877
11	SP1	chr19:39468513-39468974	GM12878	blood:	n/a	n/a
12	IRF4	chr19:39468332-39468987	GM12878	blood:	n/a	n/a
13	BCL11A	chr19:39468382-39468964	GM12878	blood:	n/a	n/a
14	BATF	chr19:39468443-39468890	GM12878	blood:	n/a	n/a
15	ATF2	chr19:39468077-39469019	GM12878	blood:	n/a	n/a
16	BCL3	chr19:39468471-39468927	GM12878	blood:	n/a	n/a
17	EBF1	chr19:39468435-39468944	GM12878	blood:	n/a	n/a
18	FOXM1	chr19:39468317-39469110	GM12878	blood:	n/a	n/a
19	NFATC1	chr19:39468452-39468929	GM12878	blood:	n/a	n/a
20	MTA3	chr19:39468312-39469196	GM12878	blood:	n/a	n/a
21	SRF	chr19:39468526-39468863	GM12878	blood:	n/a	n/a
22	PAX5	chr19:39468385-39468978	GM12878	blood:	n/a	chr19:39468868-39468877
23	STAT3	chr19:39468623-39468897	MCF10A-Er-Src	breast:	n/a	n/a
24	TCF3	chr19:39468484-39469021	GM12878	blood:	n/a	n/a
25	STAT5A	chr19:39468392-39469063	GM12878	blood:	n/a	n/a
26	POU2F2	chr19:39468489-39469007	GM12878	blood:	n/a	n/a
27	MEF2A	chr19:39468453-39469008	GM12878	blood:	n/a	chr19:39468878-39468899
28	SPI1	chr19:39468586-39468990	GM12878	blood:	n/a	n/a
29	POU2F2	chr19:39468520-39468927	GM12878	blood:	n/a	n/a
30	ELF1	chr19:39468345-39469000	GM12878	blood:	n/a	n/a
31	TCF12	chr19:39468531-39468850	GM12878	blood:	n/a	n/a
32	IRF4	chr19:39468358-39469016	GM12878	blood:	n/a	n/a
33	MEF2A	chr19:39468405-39468957	GM12878	blood:	n/a	chr19:39468878-39468899
34	ATF2	chr19:39468422-39469098	GM12878	blood:	n/a	n/a
35	RUNX3	chr19:39468389-39469118	GM12878	blood:	n/a	n/a
36	BCLAF1	chr19:39468437-39469003	GM12878	blood:	n/a	n/a
37	FOXM1	chr19:39468317-39469125	GM12878	blood:	n/a	n/a
38	EP300	chr19:39468371-39469000	GM12878	blood:	n/a	chr19:39468669-39468682
39	EBF1	chr19:39468620-39468952	GM12878	blood:	n/a	n/a
40	NFATC1	chr19:39468422-39469040	GM12878	blood:	n/a	n/a
41	PML	chr19:39468539-39468862	GM12878	blood:	n/a	n/a
42	EP300	chr19:39468486-39469023	GM12878	blood:	n/a	chr19:39468669-39468682
43	CEBPB	chr19:39468335-39469137	GM12878	blood:	n/a	n/a
44	NFIC	chr19:39468246-39469147	GM12878	blood:	n/a	n/a
45	MAX	chr19:39468564-39469202	HepG2	liver:	n/a	n/a
46	PML	chr19:39468347-39469111	GM12878	blood:	n/a	n/a
47	MAX	chr19:39468631-39469060	K562	blood:	n/a	n/a
48	PAX5	chr19:39468458-39468849	GM12878	blood:	n/a	n/a
49	TBL1XR1	chr19:39468504-39468992	GM12878	blood:	n/a	n/a
50	YY1	chr19:39468426-39468907	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39464155..39466617-chr19:39468429..39470237,2	K562	blood:

Variant related genes	Relation type
FBXO17	TF binding region
ENSG00000269190	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10425811	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28422038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6508831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250688	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39467000-39468800	Weak transcription	HSMMtube	muscle
2	chr19:39467200-39469400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39467400-39468800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:39467400-39468800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:39467400-39468800	Weak transcription	Pancreas	Pancrea
6	chr19:39467400-39468800	Weak transcription	NH-A	brain
7	chr19:39467400-39469400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:39467400-39469400	Enhancers	Fetal Intestine Small	intestine
9	chr19:39467400-39469400	Enhancers	GM12878-XiMat	blood
10	chr19:39467400-39470000	Enhancers	Fetal Intestine Large	intestine
11	chr19:39467400-39470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39467400-39471200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:39467600-39468800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:39467600-39468800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:39467600-39469200	Enhancers	A549	lung
16	chr19:39467600-39469400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:39467600-39469400	Enhancers	Liver	Liver
18	chr19:39467600-39470400	Weak transcription	K562	blood
19	chr19:39467600-39471400	Weak transcription	Brain Hippocampus Middle	brain
20	chr19:39467600-39471400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr19:39468000-39469200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr19:39468200-39469000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:39468200-39469400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr19:39468400-39468800	Flanking Active TSS	HepG2	liver
25	chr19:39468400-39469000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:39468400-39469400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr19:39468600-39468800	Enhancers	Placenta	Placenta
28	chr19:39468600-39469000	Enhancers	HUVEC	blood vessel
29	chr19:39468600-39469200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:39468600-39469200	Enhancers	Osteobl	bone
31	chr19:39468600-39469400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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