Variant report

Variant	rs73005358
Chromosome Location	chr4:174256888-174256889
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	PML	chr4:174254962-174256891	K562	blood:	n/a	n/a
2	TAL1	chr4:174253476-174257034	K562	blood:	n/a	n/a
3	MAX	chr4:174255171-174256906	MCF-7	breast:	n/a	chr4:174256491-174256500 chr4:174256443-174256453
4	MTA3	chr4:174254954-174257023	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:174252562-174257085	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr4:174256180-174256902	K562	blood:	n/a	n/a
7	POLR2A	chr4:174254512-174256999	PFSK-1	brain:	n/a	n/a
8	MAFK	chr4:174256200-174256926	K562	blood:	n/a	n/a
9	TRIM28	chr4:174254951-174257024	K562	blood:	n/a	n/a
10	SIN3A	chr4:174254400-174256958	H1-hESC	embryonic stem cell:	n/a	chr4:174254887-174254900 chr4:174254884-174254893
11	POLR2A	chr4:174254496-174257002	K562	blood:	n/a	n/a
12	POLR2A	chr4:174253089-174257840	PBDE	blood:	n/a	n/a
13	BRCA1	chr4:174256289-174257163	Hela-S3	cervix:	n/a	n/a
14	MAX	chr4:174254939-174256920	SK-N-SH	brain:	n/a	chr4:174256491-174256500 chr4:174254939-174254949 chr4:174256443-174256453
15	POLR2A	chr4:174253943-174256995	K562	blood:	n/a	n/a
16	MYC	chr4:174254841-174257107	K562	blood:	n/a	chr4:174256491-174256500 chr4:174254939-174254949 chr4:174256443-174256453
17	SIN3AK20	chr4:174255020-174256910	MCF-7	breast:	n/a	n/a
18	MYC	chr4:174254707-174257019	K562	blood:	n/a	chr4:174256491-174256500 chr4:174254939-174254949 chr4:174256443-174256453
19	POLR2A	chr4:174254982-174256903	U87	brain:	n/a	n/a
20	TEAD4	chr4:174256176-174256932	HepG2	liver:	n/a	n/a
21	POLR2A	chr4:174254944-174256913	Hela-S3	cervix:	n/a	n/a
22	HCFC1	chr4:174255101-174257134	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr4:174241673-174256923	K562	blood:	n/a	n/a
24	POLR2A	chr4:174253021-174256974	HepG2	liver:	n/a	n/a
25	POLR2A	chr4:174253936-174256945	HepG2	liver:	n/a	n/a
26	MAX	chr4:174255377-174256896	H1-hESC	embryonic stem cell:	n/a	chr4:174256491-174256500 chr4:174256443-174256453
27	RELA	chr4:174255244-174256896	GM18951	blood:	n/a	chr4:174255878-174255887 chr4:174255878-174255887
28	JUND	chr4:174255172-174256920	K562	blood:	n/a	chr4:174255787-174255796 chr4:174256244-174256253 chr4:174255601-174255610
29	POLR2A	chr4:174253875-174256979	HL-60	blood:	n/a	n/a
30	STAT3	chr4:174256376-174256919	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr4:174255011-174256899	U87	brain:	n/a	n/a
32	TBP	chr4:174254991-174256953	K562	blood:	n/a	n/a
33	POLR2A	chr4:174253253-174257499	MCF10A-Er-Src	breast:	n/a	n/a
34	SIN3AK20	chr4:174254487-174256888	SK-N-SH	brain:	n/a	n/a
35	MXI1	chr4:174252924-174257416	SK-N-SH	brain:	n/a	n/a
36	BHLHE40	chr4:174255101-174256964	K562	blood:	n/a	chr4:174256498-174256514 chr4:174256506-174256522 chr4:174255227-174255243 chr4:174256526-174256542
37	FOXM1	chr4:174254925-174256909	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr4:174252651-174256931	GM12891	blood:	n/a	n/a
39	POLR2A	chr4:174253870-174256895	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr4:174253956-174257087	IMR90	lung:	n/a	n/a
41	POLR2A	chr4:174254988-174256897	U87	brain:	n/a	n/a
42	MXI1	chr4:174255329-174257030	K562	blood:	n/a	n/a
43	POLR2A	chr4:174254961-174256973	Hela-S3	cervix:	n/a	n/a
44	IRF1	chr4:174255273-174257195	K562	blood:	n/a	chr4:174256412-174256426 chr4:174256438-174256452 chr4:174255634-174255648
45	TEAD4	chr4:174255159-174257059	K562	blood:	n/a	n/a
46	POLR2A	chr4:174254003-174256945	HCT-116	colon:	n/a	n/a
47	POLR2A	chr4:174253468-174256959	K562	blood:	n/a	n/a
48	POLR2A	chr4:174254227-174256902	K562	blood:	n/a	n/a
49	CHD1	chr4:174255046-174256914	H1-hESC	embryonic stem cell:	n/a	n/a
50	TCF12	chr4:174255073-174256965	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:174088355..174091772-chr4:174254077..174258410,8	K562	blood:
2	chr4:174252933..174259053-chr4:174284716..174299463,25	MCF-7	breast:
3	chr12:56435584..56436188-chr4:174256094..174256905,2	Hela-S3	cervix:
4	chr4:174088713..174091772-chr4:174254390..174258410,4	K562	blood:
5	chr4:174256552..174259513-chr4:174261559..174263260,2	MCF-7	breast:
6	chr4:174250771..174257645-chr4:174286907..174294441,15	MCF-7	breast:
7	chr4:174245727..174260507-chr4:174283013..174295498,65	K562	blood:
8	chr4:174255732..174257392-chr4:174326183..174328039,2	MCF-7	breast:
9	chr4:174248778..174262653-chr4:174278408..174298501,82	K562	blood:
10	chr4:174256106..174257002-chrX:47092521..47093108,2	Hela-S3	cervix:

Variant related genes	Relation type
HMGB2	TF binding region
ENSG00000164106	Chromatin interaction
ENSG00000272870	Chromatin interaction
ENSG00000102226	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000164105	Chromatin interaction
ENSG00000109586	Chromatin interaction
ENSG00000245213	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17059268	0.88[ASN][1000 genomes]
rs17059272	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17059281	0.88[ASN][1000 genomes]
rs28368237	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28699371	0.84[ASN][1000 genomes]
rs57572680	0.88[ASN][1000 genomes]
rs59212575	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59926654	0.88[ASN][1000 genomes]
rs60050553	0.84[ASN][1000 genomes]
rs6833097	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6834063	0.88[ASN][1000 genomes]
rs6839839	0.84[ASN][1000 genomes]
rs72999541	0.88[ASN][1000 genomes]
rs73001514	0.84[ASN][1000 genomes]
rs73001532	0.84[ASN][1000 genomes]
rs73001537	0.84[ASN][1000 genomes]
rs73001546	0.88[ASN][1000 genomes]
rs73001558	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73003339	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73003345	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73005344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73005350	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73005351	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73005359	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7658147	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7681398	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7682997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7689758	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][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	nsv966552	chr4:174248506-174259305	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174253000-174257000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:174253000-174257200	Active TSS	Fetal Brain Female	brain
3	chr4:174253200-174257000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:174253400-174257400	Active TSS	NHLF	lung
5	chr4:174253600-174257000	Active TSS	Fetal Muscle Trunk	muscle
6	chr4:174253800-174257000	Active TSS	Placenta Amnion	Placenta Amnion
7	chr4:174253800-174257000	Active TSS	Right Ventricle	heart
8	chr4:174253800-174257400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:174254000-174257000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:174254200-174257000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:174254200-174257000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:174254200-174257000	Active TSS	Fetal Intestine Small	intestine
13	chr4:174254200-174257000	Active TSS	Stomach Smooth Muscle	stomach
14	chr4:174254200-174257200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr4:174254400-174257000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr4:174254400-174257000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:174254400-174257000	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr4:174254400-174257000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:174254400-174257000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:174254400-174257000	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr4:174254400-174257000	Active TSS	Brain Substantia Nigra	brain
22	chr4:174254400-174257000	Active TSS	Placenta	Placenta
23	chr4:174254400-174257000	Active TSS	Fetal Stomach	stomach
24	chr4:174254400-174257000	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr4:174254400-174257000	Active TSS	Rectal Smooth Muscle	rectum
26	chr4:174254400-174257200	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr4:174254400-174257200	Active TSS	Fetal Intestine Large	intestine
28	chr4:174254400-174257200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr4:174254400-174257200	Active TSS	A549	lung
30	chr4:174254400-174257800	Active TSS	Thymus	Thymus
31	chr4:174254600-174257000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:174254600-174257000	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr4:174254600-174257000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:174254600-174257000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:174254600-174257200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr4:174254600-174257200	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr4:174254600-174257200	Active TSS	GM12878-XiMat	blood
38	chr4:174254600-174257800	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr4:174254800-174257000	Active TSS	Brain Germinal Matrix	brain
40	chr4:174254800-174257000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr4:174254800-174257000	Active TSS	Fetal Brain Male	brain
42	chr4:174254800-174257200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:174254800-174257200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:174254800-174257400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:174254800-174257600	Active TSS	Fetal Thymus	thymus
46	chr4:174254800-174257600	Active TSS	K562	blood
47	chr4:174255400-174257200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:174255600-174257000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:174256000-174257000	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr4:174256200-174257200	Flanking Active TSS	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links