Variant report

Variant	rs72927928
Chromosome Location	chr4:130016489-130016490
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	TBP	chr4:130016436-130016829	K562	blood:	n/a	n/a
2	JUND	chr4:130016361-130017886	K562	blood:	n/a	chr4:130017505-130017517 chr4:130017411-130017425
3	STAT3	chr4:130016408-130016565	MCF10A-Er-Src	breast:	n/a	n/a
4	KAP1	chr4:130016192-130016743	K562	blood:	n/a	n/a
5	TBL1XR1	chr4:130015970-130017767	K562	blood:	n/a	n/a
6	IRF1	chr4:130016415-130017935	K562	blood:	n/a	chr4:130017752-130017761 chr4:130017569-130017583 chr4:130017543-130017557 chr4:130017565-130017579 chr4:130017569-130017579 chr4:130017750-130017760 chr4:130017561-130017581
7	ARID3A	chr4:130015591-130017978	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:130012621..130015537-chr4:130015842..130017627,2	K562	blood:
2	chr4:128703531..128705249-chr4:130014655..130017577,2	K562	blood:
3	chr4:129731090..129733904-chr4:130015000..130016574,3	K562	blood:
4	chr4:129730340..129733748-chr4:130013373..130016609,5	K562	blood:

Variant related genes	Relation type
SCLT1	TF binding region
C4orf33	TF binding region
ENSG00000151466	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000164070	Chromatin interaction
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs56219732	1.00[AMR][1000 genomes]
rs56765848	0.90[AFR][1000 genomes]
rs58051833	0.90[AFR][1000 genomes]
rs59285303	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59715472	0.90[AFR][1000 genomes]
rs61702015	0.90[AFR][1000 genomes]
rs72922050	0.90[AFR][1000 genomes]
rs72922052	0.90[AFR][1000 genomes]
rs72922062	0.90[AFR][1000 genomes]
rs72922075	0.90[AFR][1000 genomes]
rs72922078	0.90[AFR][1000 genomes]
rs72922083	0.90[AFR][1000 genomes]
rs72922086	0.90[AFR][1000 genomes]
rs72922093	0.90[AFR][1000 genomes]
rs72922097	0.90[AFR][1000 genomes]
rs72922099	0.90[AFR][1000 genomes]
rs72922102	0.90[AFR][1000 genomes]
rs72922806	1.00[AMR][1000 genomes]
rs72924103	0.90[AFR][1000 genomes]
rs72924109	0.90[AFR][1000 genomes]
rs72924111	0.90[AFR][1000 genomes]
rs72924115	0.90[AFR][1000 genomes]
rs72924122	0.90[AFR][1000 genomes]
rs72924138	0.90[AFR][1000 genomes]
rs72924154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72924157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72924160	0.90[AFR][1000 genomes]
rs72924167	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72924180	0.90[AFR][1000 genomes]
rs72924185	0.90[AFR][1000 genomes]
rs72926010	0.90[AFR][1000 genomes]
rs72926011	0.90[AFR][1000 genomes]
rs72926013	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72926017	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72926020	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72926029	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72926030	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72926036	0.90[AFR][1000 genomes]
rs72926056	0.90[AFR][1000 genomes]
rs72926071	0.90[AFR][1000 genomes]
rs72926072	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72926087	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72926090	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72927922	1.00[AMR][1000 genomes]
rs72927936	1.00[AFR][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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130012800-130018600	Active TSS	K562	blood
2	chr4:130014800-130017200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:130014800-130017200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:130015000-130017200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:130015000-130017200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:130015000-130017200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:130015000-130017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:130015200-130017000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:130015200-130017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:130015200-130017000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:130015200-130017200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:130015200-130017200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:130015200-130017200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:130015200-130017200	Weak transcription	Esophagus	oesophagus
15	chr4:130015200-130017200	Weak transcription	Placenta	Placenta
16	chr4:130015200-130017200	Weak transcription	Left Ventricle	heart
17	chr4:130015200-130017200	Weak transcription	Lung	lung
18	chr4:130015200-130017200	Weak transcription	Pancreas	Pancrea
19	chr4:130015200-130017200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:130015200-130017200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:130015200-130017200	Weak transcription	Small Intestine	intestine
22	chr4:130015200-130017200	Weak transcription	HSMM	muscle
23	chr4:130015200-130017200	Weak transcription	HSMMtube	muscle
24	chr4:130015400-130016600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:130015400-130016800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr4:130015400-130016800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:130015400-130017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:130015400-130017000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:130015400-130017000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:130015400-130017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:130015400-130017000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:130015400-130017000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:130015400-130017000	Enhancers	Primary T cells from cord blood	blood
34	chr4:130015400-130017000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:130015400-130017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:130015400-130017000	Weak transcription	Liver	Liver
37	chr4:130015400-130017000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:130015400-130017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:130015400-130017000	Weak transcription	Colonic Mucosa	Colon
40	chr4:130015400-130017000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:130015400-130017000	Weak transcription	Fetal Intestine Large	intestine
42	chr4:130015400-130017000	Weak transcription	Fetal Thymus	thymus
43	chr4:130015400-130017000	Weak transcription	Ovary	ovary
44	chr4:130015400-130017000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr4:130015400-130017000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:130015400-130017000	Weak transcription	Right Atrium	heart
47	chr4:130015400-130017000	Weak transcription	Stomach Mucosa	stomach
48	chr4:130015400-130017000	Weak transcription	A549	lung
49	chr4:130015400-130017200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:130015400-130017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links