Variant report

Variant	rs6798092
Chromosome Location	chr3:53136622-53136623
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	POLR2A	chr3:53136615-53137096	GM12892	blood:	n/a	n/a
2	MTA3	chr3:53136581-53137088	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:53136552-53137153	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:53136622-53136866	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:53136518-53137132	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53127951..53129779-chr3:53135575..53137471,2	K562	blood:
2	chr3:53132181..53134666-chr3:53136368..53138865,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272305	TF binding region
ENSG00000272305	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3891626	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58624586	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6785768	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6787566	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965386	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965387	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965388	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965394	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965401	0.94[AFR][1000 genomes];1.00[AMR][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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53107800-53151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:53117800-53147200	Weak transcription	Psoas Muscle	Psoas
3	chr3:53119000-53154200	Weak transcription	Stomach Mucosa	stomach
4	chr3:53120400-53138600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:53120800-53138400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:53120800-53144400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:53121400-53142600	Strong transcription	Stomach Smooth Muscle	stomach
8	chr3:53121800-53137800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:53122400-53136800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:53122400-53143200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:53122800-53152200	Weak transcription	Small Intestine	intestine
12	chr3:53123200-53138800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:53123200-53148600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:53124200-53151600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:53124800-53139400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:53127000-53154200	Weak transcription	Right Atrium	heart
17	chr3:53127400-53144000	Weak transcription	Fetal Heart	heart
18	chr3:53128600-53137200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:53130000-53136800	Strong transcription	Fetal Intestine Small	intestine
20	chr3:53130800-53146400	Strong transcription	Fetal Intestine Large	intestine
21	chr3:53131200-53139200	Strong transcription	Dnd41	blood
22	chr3:53131400-53137000	Strong transcription	Primary B cells from cord blood	blood
23	chr3:53131400-53137400	Strong transcription	Adipose Nuclei	Adipose
24	chr3:53131600-53137800	Strong transcription	Primary hematopoietic stem cells	blood
25	chr3:53131600-53138600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:53131600-53139600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr3:53131600-53140800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:53131600-53144000	Strong transcription	Liver	Liver
29	chr3:53131800-53138400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:53131800-53139400	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr3:53131800-53140800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:53132000-53137800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:53132000-53139600	Strong transcription	Aorta	Aorta
34	chr3:53132000-53139600	Strong transcription	Thymus	Thymus
35	chr3:53132000-53141800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:53132000-53148000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:53132200-53140200	Strong transcription	Right Ventricle	heart
38	chr3:53132400-53139400	Strong transcription	Ovary	ovary
39	chr3:53132400-53139800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:53132800-53139200	Strong transcription	Brain Angular Gyrus	brain
41	chr3:53133000-53138200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:53133000-53138400	Strong transcription	Gastric	stomach
43	chr3:53133000-53139600	Strong transcription	Left Ventricle	heart
44	chr3:53133400-53137200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:53133600-53136800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:53133600-53137200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:53133600-53137400	Weak transcription	Hela-S3	cervix
48	chr3:53133600-53138000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:53133600-53152600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:53133800-53137600	Weak transcription	HUVEC	blood vessel

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