Variant report

Variant	rs59133000
Chromosome Location	chr5:40798974-40798975
allele	C/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	TCF7L2	chr5:40798539-40799053	PANC-1	pancreas:	n/a	n/a
2	ZNF143	chr5:40798055-40799098	Hela-S3	cervix:	n/a	chr5:40798457-40798467 chr5:40798078-40798088 chr5:40798453-40798463 chr5:40798393-40798403
3	MAX	chr5:40797466-40799110	K562	blood:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
4	POLR2A	chr5:40797493-40799044	K562	blood:	n/a	n/a
5	POLR2A	chr5:40798340-40799094	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr5:40798846-40799004	K562	blood:	n/a	n/a
7	POLR2A	chr5:40797547-40799101	K562	blood:	n/a	n/a
8	MYC	chr5:40798701-40799027	MCF10A-Er-Src	breast:	n/a	n/a
9	CHD2	chr5:40797532-40799022	K562	blood:	n/a	chr5:40798490-40798500 chr5:40798851-40798861
10	CTCF	chr5:40798095-40799543	K562	blood:	n/a	chr5:40798438-40798451 chr5:40798442-40798451 chr5:40798589-40798598
11	MAX	chr5:40797593-40799127	HepG2	liver:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
12	TBL1XR1	chr5:40797271-40799794	K562	blood:	n/a	n/a
13	MAZ	chr5:40797297-40799432	IMR90	lung:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
14	CTCF	chr5:40798880-40799030	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr5:40798972-40799061	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr5:40798940-40799090	NB4	blood:	n/a	n/a
17	RCOR1	chr5:40797576-40800142	K562	blood:	n/a	n/a
18	TAF1	chr5:40797613-40799035	K562	blood:	n/a	n/a
19	CTCF	chr5:40798860-40799010	NHDF-neo	bronchial:	n/a	n/a
20	RAD21	chr5:40798168-40799131	H1-hESC	embryonic stem cell:	n/a	chr5:40798739-40798749 chr5:40798655-40798665
21	CTCF	chr5:40798920-40799070	HAc	cerebellar:	n/a	n/a
22	POLR2A	chr5:40797470-40799107	Hela-S3	cervix:	n/a	n/a
23	JUN	chr5:40798838-40799311	K562	blood:	n/a	chr5:40798855-40798864 chr5:40798847-40798856 chr5:40798854-40798863
24	ZNF384	chr5:40797479-40799069	K562	blood:	n/a	n/a
25	MAX	chr5:40797585-40799114	MCF-7	breast:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
26	NR2F2	chr5:40797970-40799245	K562	blood:	n/a	n/a
27	RAD21	chr5:40798684-40799083	SK-N-SH_RA	brain:	n/a	chr5:40798739-40798749
28	TAF1	chr5:40798739-40799052	SK-N-SH	brain:	n/a	n/a
29	ELK4	chr5:40798604-40799067	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr5:40798840-40798990	HVMF	connective:	n/a	n/a
31	SIN3AK20	chr5:40798347-40799111	MCF-7	breast:	n/a	n/a
32	ARID3A	chr5:40798896-40799811	K562	blood:	n/a	n/a
33	E2F4	chr5:40798355-40799397	MCF10A-Er-Src	breast:	n/a	chr5:40798844-40798851 chr5:40798407-40798417 chr5:40798844-40798851 chr5:40798844-40798851 chr5:40798453-40798462 chr5:40798843-40798855 chr5:40798457-40798467 chr5:40798850-40798862 chr5:40798853-40798862
34	RFX5	chr5:40797380-40799619	Hela-S3	cervix:	n/a	chr5:40797938-40797953 chr5:40797937-40797954 chr5:40798991-40798999 chr5:40797938-40797953 chr5:40797938-40797953
35	BRCA1	chr5:40797611-40799729	Hela-S3	cervix:	n/a	n/a
36	CREB1	chr5:40797960-40799120	HepG2	liver:	n/a	n/a
37	POLR2A	chr5:40797440-40799117	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr5:40797569-40799159	K562	blood:	n/a	n/a
39	POLR2A	chr5:40797404-40799287	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr5:40798880-40799030	HPAF	blood vessel:	n/a	n/a
41	CTCF	chr5:40798860-40799010	GM12865	blood:	n/a	n/a
42	EP300	chr5:40797373-40799970	K562	blood:	n/a	chr5:40798444-40798460 chr5:40797855-40797864 chr5:40797823-40797832 chr5:40799242-40799252 chr5:40798012-40798028 chr5:40797852-40797868
43	MYC	chr5:40797555-40799370	A549	lung:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
44	TCF12	chr5:40797531-40799149	A549	lung:	n/a	chr5:40798098-40798105
45	SMARCC1	chr5:40797137-40799001	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr5:40798880-40799030	HBMEC	blood vessel:	n/a	n/a
47	TEAD4	chr5:40797328-40799160	K562	blood:	n/a	n/a
48	CTCF	chr5:40798860-40799010	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr5:40798931-40798993	Kidney_OC	kidney:	n/a	n/a
50	CTCF	chr5:40798860-40799010	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:40755665..40756472-chr5:40798471..40799111,2	K562	blood:
2	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
3	chr5:40755012..40759487-chr5:40796000..40799940,8	K562	blood:
4	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
5	chr5:40778589..40781833-chr5:40798494..40800242,3	K562	blood:
6	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
7	chr5:40798384..40799086-chr5:40834783..40835322,2	MCF-7	breast:
8	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
9	chr5:40778589..40781225-chr5:40798736..40800242,2	K562	blood:

Variant related genes	Relation type
PRKAA1	TF binding region
ENSG00000113638	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000212296	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1001684	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1002423	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1002424	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10041430	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10071679	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10074991	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122655	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11956019	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11956047	0.89[AMR][1000 genomes]
rs11957736	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13361707	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329353	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28544962	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805487	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805495	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805497	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4957352	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58692207	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58751240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59338019	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59585832	0.97[ASN][1000 genomes]
rs6868517	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7702883	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705504	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
4	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40795800-40800000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:40796200-40799600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:40796200-40799600	Active TSS	Fetal Intestine Large	intestine
4	chr5:40796400-40799200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:40796400-40800000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:40796400-40800000	Active TSS	NHLF	lung
7	chr5:40796600-40799000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:40796600-40799000	Active TSS	Stomach Mucosa	stomach
9	chr5:40796600-40799000	Active TSS	NH-A	brain
10	chr5:40796600-40799200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:40796600-40799200	Active TSS	Fetal Brain Male	brain
12	chr5:40796600-40799200	Active TSS	Fetal Intestine Small	intestine
13	chr5:40796600-40799200	Active TSS	HSMMtube	muscle
14	chr5:40796600-40799400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:40796600-40799600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:40796600-40799600	Active TSS	Ovary	ovary
17	chr5:40796600-40799800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr5:40796600-40799800	Active TSS	Fetal Kidney	kidney
19	chr5:40796600-40800000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:40796600-40800400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr5:40796800-40799000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:40796800-40799000	Active TSS	Rectal Smooth Muscle	rectum
23	chr5:40796800-40799200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:40796800-40799200	Active TSS	Aorta	Aorta
25	chr5:40796800-40799200	Active TSS	Fetal Muscle Leg	muscle
26	chr5:40796800-40799200	Active TSS	Psoas Muscle	Psoas
27	chr5:40796800-40799200	Active TSS	Right Ventricle	heart
28	chr5:40796800-40799400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:40796800-40799400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr5:40796800-40799400	Active TSS	Fetal Stomach	stomach
31	chr5:40796800-40799600	Active TSS	NHDF-Ad	bronchial
32	chr5:40797000-40799000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:40797000-40799000	Active TSS	Fetal Brain Female	brain
34	chr5:40797000-40799000	Active TSS	HSMM	muscle
35	chr5:40797000-40799200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:40797000-40799200	Active TSS	Colonic Mucosa	Colon
37	chr5:40797000-40799200	Active TSS	Fetal Muscle Trunk	muscle
38	chr5:40797000-40799200	Active TSS	Thymus	Thymus
39	chr5:40797000-40799400	Active TSS	K562	blood
40	chr5:40797000-40799800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr5:40797000-40800000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr5:40797200-40799000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr5:40797200-40799000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr5:40797200-40799000	Active TSS	Brain Germinal Matrix	brain
45	chr5:40797200-40799000	Active TSS	Brain Substantia Nigra	brain
46	chr5:40797200-40799000	Active TSS	Gastric	stomach
47	chr5:40797200-40799000	Active TSS	Lung	lung
48	chr5:40797200-40799000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr5:40797200-40799000	Active TSS	HUVEC	blood vessel
50	chr5:40797200-40799200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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