Variant report

Variant	rs62254282
Chromosome Location	chr3:53192697-53192698
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	SPI1	chr3:53192518-53193578	HL-60	blood:	n/a	chr3:53192891-53192900 chr3:53192890-53192903 chr3:53192890-53192903 chr3:53192889-53192902
2	SPI1	chr3:53192695-53193037	K562	blood:	n/a	chr3:53192891-53192900 chr3:53192890-53192903 chr3:53192890-53192903 chr3:53192889-53192902
3	SPI1	chr3:53192650-53193097	GM12891	blood:	n/a	chr3:53192891-53192900 chr3:53192890-53192903 chr3:53192890-53192903 chr3:53192889-53192902
4	SPI1	chr3:53192672-53193064	GM12878	blood:	n/a	chr3:53192891-53192900 chr3:53192890-53192903 chr3:53192890-53192903 chr3:53192889-53192902
5	SPI1	chr3:53192422-53193352	GM12878	blood:	n/a	chr3:53192891-53192900 chr3:53192890-53192903 chr3:53192890-53192903 chr3:53192889-53192902
6	SPI1	chr3:53192614-53193144	GM12891	blood:	n/a	chr3:53192891-53192900 chr3:53192890-53192903 chr3:53192890-53192903 chr3:53192889-53192902

No.	Distal block	Cell Line	Cell type
1	chr3:53191078..53192813-chr3:53254654..53256818,2	K562	blood:
2	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
3	chr16:30758613..30761206-chr3:53192006..53193731,2	MCF-7	breast:
4	chr3:53150117..53153813-chr3:53191442..53194922,3	MCF-7	breast:
5	chr3:53167017..53169952-chr3:53191720..53194469,2	K562	blood:

Variant related genes	Relation type
PRKCD	TF binding region
ENSG00000156873	Chromatin interaction
ENSG00000163933	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11924565	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1483185	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1483186	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1483187	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242305	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3773724	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3773726	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3773727	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3773731	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3773733	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57046386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775022	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6797662	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6807359	0.84[EUR][1000 genomes]
rs72537447	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7630325	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53182400-53193400	Weak transcription	Psoas Muscle	Psoas
2	chr3:53182400-53193800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:53183200-53194600	Enhancers	Gastric	stomach
4	chr3:53183400-53194600	Enhancers	Pancreas	Pancrea
5	chr3:53184200-53194400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:53184400-53193800	Enhancers	Adipose Nuclei	Adipose
7	chr3:53187800-53194600	Enhancers	Esophagus	oesophagus
8	chr3:53188000-53192800	Weak transcription	Small Intestine	intestine
9	chr3:53188800-53192800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr3:53189600-53194000	Enhancers	Stomach Mucosa	stomach
11	chr3:53190200-53193200	Weak transcription	Left Ventricle	heart
12	chr3:53190200-53194200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:53190600-53192800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr3:53190600-53194000	Enhancers	Colonic Mucosa	Colon
15	chr3:53190600-53194400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr3:53190800-53194600	Enhancers	Lung	lung
17	chr3:53191000-53192800	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr3:53191000-53193200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:53191000-53194400	Enhancers	Fetal Intestine Small	intestine
20	chr3:53191200-53193200	Enhancers	Duodenum Mucosa	Duodenum
21	chr3:53191200-53194400	Enhancers	Placenta	Placenta
22	chr3:53191400-53193400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:53191400-53194400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:53191400-53194400	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:53191400-53194400	Enhancers	Fetal Intestine Large	intestine
26	chr3:53191600-53193200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:53191600-53193400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:53191600-53193400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:53191600-53193400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:53191600-53194000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:53191800-53192800	Enhancers	Brain Anterior Caudate	brain
32	chr3:53191800-53193200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:53191800-53194200	Enhancers	Brain Hippocampus Middle	brain
34	chr3:53191800-53194200	Weak transcription	HMEC	breast
35	chr3:53191800-53194400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:53191800-53194400	Enhancers	Right Ventricle	heart
37	chr3:53192000-53192800	Weak transcription	Right Atrium	heart
38	chr3:53192000-53193400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:53192000-53194600	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:53192200-53192800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:53192200-53194000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:53192200-53194400	Enhancers	Primary B cells from cord blood	blood
43	chr3:53192400-53192800	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:53192400-53193400	Enhancers	Hela-S3	cervix
45	chr3:53192400-53193600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr3:53192400-53194000	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr3:53192400-53194600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:53192400-53194600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:53192400-53194600	Enhancers	Liver	Liver
50	chr3:53192600-53192800	Enhancers	Brain Angular Gyrus	brain

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