Variant report

Variant	rs1345777
Chromosome Location	chr5:50263788-50263789
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	SPI1	chr5:50263595-50263806	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:50261628-50264919	H1-neurons	neurons:	n/a	n/a
3	SUZ12	chr5:50262485-50266469	NT2-D1	testis:	n/a	n/a
4	RAD21	chr5:50263452-50263856	SK-N-SH_RA	brain:	n/a	n/a
5	IRF1	chr5:50263534-50263874	K562	blood:	n/a	chr5:50263693-50263707 chr5:50263701-50263715 chr5:50263693-50263710 chr5:50263696-50263709 chr5:50263695-50263715 chr5:50263699-50263713 chr5:50263705-50263714 chr5:50263696-50263709 chr5:50263695-50263706 chr5:50263696-50263707 chr5:50263701-50263712 chr5:50263696-50263710 chr5:50263696-50263709 chr5:50263697-50263711
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	SMC3	chr5:50263549-50263868	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:50263381-50263942	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr5:50261875-50264646	H1-neurons	neurons:	n/a	n/a
10	RAD21	chr5:50263476-50263812	Hela-S3	cervix:	n/a	n/a
11	CTBP2	chr5:50263275-50263805	H1-hESC	embryonic stem cell:	n/a	n/a
12	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: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10035173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054150	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11746939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163606	0.98[ASN][1000 genomes]
rs151986	0.90[AFR][1000 genomes]
rs151997	0.94[ASW][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs152817	0.92[YRI][hapmap]
rs2069021	0.86[JPT][hapmap]
rs250230	0.85[YRI][hapmap]
rs27247	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs27249	0.94[ASW][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35056981	0.87[EUR][1000 genomes]
rs3846498	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3846499	0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3846500	0.94[ASW][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4429809	0.86[JPT][hapmap]
rs62367392	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367393	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635788	0.83[AFR][1000 genomes]
rs6870880	0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6882235	0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7720791	0.86[JPT][hapmap]
rs9292165	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	chr5:50261600-50264400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:50262000-50264000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:50262200-50263800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr5:50262200-50264000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:50262200-50264200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr5:50262400-50263800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
11	chr5:50262600-50264200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr5:50262600-50264400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
13	chr5:50262600-50265200	Bivalent/Poised TSS	NHDF-Ad	bronchial
14	chr5:50262600-50266000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr5:50262600-50266200	Bivalent/Poised TSS	Fetal Stomach	stomach
16	chr5:50262800-50264000	Bivalent/Poised TSS	HSMMtube	muscle
17	chr5:50262800-50264200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
18	chr5:50262800-50264600	Bivalent/Poised TSS	Thymus	Thymus
19	chr5:50262800-50265200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:50262800-50265200	Bivalent/Poised TSS	Psoas Muscle	Psoas
21	chr5:50262800-50265400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr5:50262800-50266200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
23	chr5:50263000-50263800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:50263000-50263800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:50263000-50263800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
26	chr5:50263000-50263800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
27	chr5:50263000-50263800	Bivalent/Poised TSS	HSMM	muscle
28	chr5:50263000-50265000	Bivalent/Poised TSS	Left Ventricle	heart
29	chr5:50263000-50265200	Active TSS	Right Atrium	heart
30	chr5:50263000-50266000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
31	chr5:50263000-50266000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
32	chr5:50263200-50263800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr5:50263200-50263800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:50263200-50263800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
35	chr5:50263200-50263800	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
36	chr5:50263200-50263800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
37	chr5:50263200-50263800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
38	chr5:50263200-50263800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
39	chr5:50263200-50263800	Bivalent/Poised TSS	Esophagus	oesophagus
40	chr5:50263200-50263800	Flanking Active TSS	Right Ventricle	heart
41	chr5:50263200-50264000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
42	chr5:50263200-50264000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:50263200-50264000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:50263200-50264000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
45	chr5:50263200-50264000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr5:50263200-50264000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr5:50263200-50264000	Bivalent/Poised TSS	Fetal Thymus	thymus
48	chr5:50263200-50264000	Bivalent/Poised TSS	Stomach Mucosa	stomach
49	chr5:50263200-50264000	Active TSS	Hela-S3	cervix
50	chr5:50263200-50265600	Active TSS	Stomach Smooth Muscle	stomach

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