Variant report

Variant	rs58676472
Chromosome Location	chr5:50264744-50264745
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	SIN3A	chr5:50264730-50265502	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:50264217-50264758	SK-N-SH	brain:	n/a	n/a
3	SP1	chr5:50264363-50264900	H1-hESC	embryonic stem cell:	n/a	chr5:50264487-50264494
4	POLR2A	chr5:50261628-50264919	H1-neurons	neurons:	n/a	n/a
5	SUZ12	chr5:50262485-50266469	NT2-D1	testis:	n/a	n/a
6	GATA2	chr5:50263552-50266094	SH-SY5Y	brain:	n/a	chr5:50264176-50264197 chr5:50264179-50264195 chr5:50264183-50264192 chr5:50264183-50264192 chr5:50264164-50264171 chr5:50263968-50263975 chr5:50264179-50264195 chr5:50264859-50264868 chr5:50264182-50264192 chr5:50266034-50266043
7	REST	chr5:50261713-50266474	H1-neurons	neurons:	n/a	chr5:50264435-50264449 chr5:50264118-50264138 chr5:50264118-50264138 chr5:50265442-50265452 chr5:50264121-50264134

Variant related genes	Relation type
ENSG00000250360	TF binding region
ENSG00000248918	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10461650	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10940614	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11948423	0.81[AFR][1000 genomes]
rs11960414	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11960464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1374038	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17219112	0.89[ASN][1000 genomes]
rs2404464	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3899258	0.81[AMR][1000 genomes]
rs58944804	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62367363	0.81[AFR][1000 genomes]
rs62367389	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62367390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62367391	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72758253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs983098	0.92[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	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:50260200-50265000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:50261400-50266400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:50261400-50266400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr5:50262600-50265200	Bivalent/Poised TSS	NHDF-Ad	bronchial
6	chr5:50262600-50266000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr5:50262600-50266200	Bivalent/Poised TSS	Fetal Stomach	stomach
8	chr5:50262800-50265200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:50262800-50265200	Bivalent/Poised TSS	Psoas Muscle	Psoas
10	chr5:50262800-50265400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
11	chr5:50262800-50266200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
12	chr5:50263000-50265000	Bivalent/Poised TSS	Left Ventricle	heart
13	chr5:50263000-50265200	Active TSS	Right Atrium	heart
14	chr5:50263000-50266000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
15	chr5:50263000-50266000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr5:50263200-50265600	Active TSS	Stomach Smooth Muscle	stomach
17	chr5:50263200-50265800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
18	chr5:50263200-50265800	Bivalent Enhancer	Fetal Heart	heart
19	chr5:50263200-50266000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
20	chr5:50263200-50266000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
21	chr5:50263400-50265400	Flanking Bivalent TSS/Enh	Liver	Liver
22	chr5:50263400-50265600	Bivalent/Poised TSS	Aorta	Aorta
23	chr5:50263400-50265800	Bivalent Enhancer	Fetal Brain Male	brain
24	chr5:50263400-50265800	Active TSS	Gastric	stomach
25	chr5:50263400-50266000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:50263600-50265200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:50263600-50266000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr5:50263600-50266000	Bivalent Enhancer	Fetal Lung	lung
29	chr5:50263800-50265200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
30	chr5:50263800-50265200	Bivalent Enhancer	Fetal Intestine Small	intestine
31	chr5:50263800-50265200	Enhancers	Pancreas	Pancrea
32	chr5:50263800-50265400	Bivalent Enhancer	Fetal Intestine Large	intestine
33	chr5:50263800-50265600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:50263800-50265600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr5:50263800-50265600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
36	chr5:50263800-50265800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr5:50263800-50265800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
38	chr5:50263800-50266000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr5:50263800-50266000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
40	chr5:50263800-50266000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
41	chr5:50263800-50266200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr5:50263800-50266400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr5:50264000-50265000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
44	chr5:50264000-50265000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
45	chr5:50264000-50265200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:50264000-50265200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:50264000-50265200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
48	chr5:50264000-50265400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:50264000-50265400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
50	chr5:50264000-50266000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood

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