Variant report

Variant	rs72905053
Chromosome Location	chr4:99831534-99831535
allele	A/C
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	GATA3	chr4:99831029-99831670	SK-N-SH	brain:	n/a	chr4:99831330-99831346 chr4:99831333-99831343 chr4:99831327-99831348 chr4:99831334-99831343 chr4:99831334-99831341
2	GATA3	chr4:99831018-99831609	SK-N-SH	brain:	n/a	chr4:99831330-99831346 chr4:99831333-99831343 chr4:99831327-99831348 chr4:99831334-99831343 chr4:99831334-99831341

No.	Distal block	Cell Line	Cell type
1	chr4:99831130..99833750-chr4:99845211..99847015,2	MCF-7	breast:
2	chr4:99821499..99832064-chr4:99845860..99851281,12	MCF-7	breast:
3	chr4:99830466..99832441-chr4:99915754..99918294,2	K562	blood:
4	chr4:99830941..99833130-chr4:99915425..99918294,2	K562	blood:

Variant related genes	Relation type
TBCAP3	TF binding region
ENSG00000263923	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000238449	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs62323189	0.86[AFR][1000 genomes]
rs6814029	1.00[AMR][1000 genomes]
rs6828340	0.90[AMR][1000 genomes]
rs6833074	1.00[AMR][1000 genomes]
rs6834230	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893533	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893538	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893541	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905036	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905048	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7693840	0.95[AFR][1000 genomes];1.00[AMR][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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99802800-99849000	Weak transcription	Aorta	Aorta
2	chr4:99804400-99848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:99804600-99838400	Weak transcription	Esophagus	oesophagus
4	chr4:99805200-99832000	Weak transcription	Spleen	Spleen
5	chr4:99807200-99849000	Weak transcription	Colonic Mucosa	Colon
6	chr4:99807800-99832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:99808000-99841400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:99808600-99849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:99815800-99848200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:99816600-99847200	Weak transcription	Fetal Brain Male	brain
11	chr4:99822800-99831800	Weak transcription	Fetal Stomach	stomach
12	chr4:99823000-99835600	Weak transcription	Adipose Nuclei	Adipose
13	chr4:99823000-99836000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:99823000-99841600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:99823000-99842600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:99823000-99845600	Weak transcription	Hela-S3	cervix
17	chr4:99823000-99847200	Weak transcription	Thymus	Thymus
18	chr4:99823000-99848800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:99823000-99849000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:99823000-99849200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:99823200-99831600	Weak transcription	Fetal Lung	lung
22	chr4:99823200-99839600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:99823200-99847800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:99823200-99848000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:99823200-99848600	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:99823200-99848800	Weak transcription	Placenta	Placenta
27	chr4:99824200-99846800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:99825200-99832200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr4:99825200-99832400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr4:99825200-99841400	Weak transcription	Psoas Muscle	Psoas
31	chr4:99825800-99831800	Weak transcription	Pancreas	Pancrea
32	chr4:99825800-99837200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:99826000-99831800	Weak transcription	Lung	lung
34	chr4:99826400-99832200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr4:99827000-99841000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:99827000-99848200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:99827200-99832400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr4:99827200-99846000	Weak transcription	Fetal Intestine Large	intestine
39	chr4:99827400-99831800	Weak transcription	NHLF	lung
40	chr4:99827400-99837800	Weak transcription	HepG2	liver
41	chr4:99827600-99838600	Weak transcription	HSMM	muscle
42	chr4:99827600-99846400	Weak transcription	NH-A	brain
43	chr4:99827600-99846600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:99828000-99832000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr4:99828000-99832200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:99828000-99832200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:99828000-99841200	Weak transcription	Osteobl	bone
48	chr4:99828200-99831800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:99828600-99832000	Enhancers	Colon Smooth Muscle	Colon
50	chr4:99828800-99832200	Enhancers	Rectal Smooth Muscle	rectum

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