Variant report

Variant	rs58914641
Chromosome Location	chr3:48936963-48936964
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	MAZ	chr3:48935654-48937063	IMR90	lung:	n/a	chr3:48936328-48936338
2	RUNX3	chr3:48936758-48937151	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48935994-48937070	Raji	blood:	n/a	n/a
4	RUNX3	chr3:48935739-48937156	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:48935874-48937089	GM12891	blood:	n/a	n/a
6	STAT5A	chr3:48935819-48937028	GM12878	blood:	n/a	chr3:48936427-48936439
7	MXI1	chr3:48934833-48937016	IMR90	lung:	n/a	n/a
8	MTA3	chr3:48935428-48936981	GM12878	blood:	n/a	n/a
9	EP300	chr3:48936148-48937004	GM12878	blood:	n/a	chr3:48936299-48936308 chr3:48936296-48936305 chr3:48936298-48936307
10	MXI1	chr3:48935171-48937075	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48933374..48937590-chr3:48954193..48958596,7	K562	blood:
2	chr19:19626804..19627575-chr3:48936168..48936977,2	Hela-S3	cervix:
3	chr3:48884613..48886690-chr3:48935919..48937613,2	K562	blood:

Variant related genes	Relation type
SLC25A20	TF binding region
ENSG00000177479	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000221883	Chromatin interaction
ENSG00000224424	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000114302	Chromatin interaction
ENSG00000258674	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13318132	1.00[EUR][1000 genomes]
rs14828	1.00[EUR][1000 genomes]
rs28523319	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs4527417	1.00[EUR][1000 genomes]
rs58708931	1.00[EUR][1000 genomes]
rs58835493	1.00[EUR][1000 genomes]
rs58998762	1.00[EUR][1000 genomes]
rs59352296	1.00[EUR][1000 genomes]
rs60338814	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60352528	1.00[EUR][1000 genomes]
rs61008775	1.00[EUR][1000 genomes]
rs61744082	1.00[EUR][1000 genomes]
rs6791777	1.00[EUR][1000 genomes]
rs72930094	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72931155	1.00[EUR][1000 genomes]
rs72931157	1.00[EUR][1000 genomes]
rs72931171	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72934791	1.00[EUR][1000 genomes]
rs72936804	1.00[EUR][1000 genomes]
rs72936810	1.00[EUR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830466	1.00[EUR][1000 genomes]
rs73830478	1.00[EUR][1000 genomes]
rs73833525	1.00[EUR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9820609	1.00[EUR][1000 genomes]
rs9833422	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9860187	1.00[EUR][1000 genomes]
rs9875203	1.00[EUR][1000 genomes]
rs9876812	1.00[EUR][1000 genomes]
rs9877045	1.00[EUR][1000 genomes]
rs9882714	0.83[AMR][1000 genomes];1.00[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	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48934400-48937000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:48934800-48937000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr3:48935800-48937000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:48935800-48937000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:48936200-48937000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:48936400-48937000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:48936400-48937000	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr3:48936400-48937000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr3:48936400-48937000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr3:48936400-48937000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:48936400-48937000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:48936400-48937000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:48936400-48937000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr3:48936400-48937000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr3:48936400-48937000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:48936400-48937000	Flanking Active TSS	Dnd41	blood
17	chr3:48936400-48937000	Flanking Active TSS	GM12878-XiMat	blood
18	chr3:48936400-48937200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:48936400-48937200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:48936400-48937200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:48936600-48937000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:48936600-48937000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr3:48936600-48937000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:48936600-48937000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:48936600-48937000	Enhancers	Gastric	stomach
26	chr3:48936600-48937000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:48936600-48937000	Enhancers	Spleen	Spleen
28	chr3:48936600-48937000	Enhancers	HMEC	breast
29	chr3:48936600-48937000	Flanking Active TSS	K562	blood
30	chr3:48936600-48937200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:48936600-48937200	Enhancers	Primary B cells from peripheral blood	blood
32	chr3:48936600-48937200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:48936600-48938000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:48936600-48954800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:48936600-48954800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:48936800-48937000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:48936800-48937000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr3:48936800-48937000	Enhancers	Primary B cells from cord blood	blood
39	chr3:48936800-48937000	Enhancers	Primary hematopoietic stem cells	blood
40	chr3:48936800-48937000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:48936800-48937000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:48936800-48937000	Enhancers	Adipose Nuclei	Adipose
43	chr3:48936800-48937000	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:48936800-48937000	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:48936800-48937000	Enhancers	HepG2	liver
46	chr3:48936800-48937000	Enhancers	NHEK	skin
47	chr3:48936800-48937200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:48936800-48937200	Enhancers	Thymus	Thymus
49	chr3:48936800-48937200	Enhancers	Hela-S3	cervix
50	chr3:48936800-48937200	Enhancers	Monocytes-CD14+_RO01746	blood

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