Variant report

Variant	rs28370070
Chromosome Location	chr1:223937771-223937772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr1:223936280-223937855	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr1:223937680-223937830	GM12873	blood:	n/a	n/a
3	POLR2A	chr1:223937770-223937808	HUVEC	blood vessel:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223925259..223927259-chr1:223937310..223938830,2	K562	blood:
2	chr1:223936854..223938919-chr1:223960180..223962303,2	K562	blood:
3	chr1:223924785..223927259-chr1:223936900..223938830,2	K562	blood:
4	chr1:223937050..223939736-chr1:223946719..223949161,2	K562	blood:
5	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:
6	chr1:223931041..223933395-chr1:223937050..223938620,2	K562	blood:
7	chr1:223936472..223939236-chr1:224031329..224033727,2	K562	blood:
8	chr1:223915826..223918177-chr1:223937169..223939533,2	K562	blood:
9	chr1:223898965..223904523-chr1:223935616..223939096,7	MCF-7	breast:
10	chr1:223884772..223887549-chr1:223936018..223938654,2	MCF-7	breast:
11	chr1:223899274..223906539-chr1:223934896..223938666,15	MCF-7	breast:
12	chr1:223937021..223937991-chr1:223946905..223947482,2	K562	blood:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1153961	0.83[ASN][1000 genomes]
rs1153964	0.83[ASN][1000 genomes]
rs1222078	0.83[ASN][1000 genomes]
rs1222080	0.83[ASN][1000 genomes]
rs1222130	0.83[ASN][1000 genomes]
rs2298256	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28370098	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3754086	0.85[ASN][1000 genomes]
rs6688042	0.83[AMR][1000 genomes]
rs6704537	0.82[ASN][1000 genomes]
rs7540481	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223937800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:223936800-223938200	Weak transcription	Spleen	Spleen
7	chr1:223936800-223942800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:223936800-223947400	Weak transcription	Fetal Brain Male	brain
9	chr1:223936800-223954400	Strong transcription	HSMM	muscle
10	chr1:223937000-223937800	Weak transcription	Primary T cells from cord blood	blood
11	chr1:223937000-223937800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:223937000-223937800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:223937000-223938000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:223937000-223938000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:223937000-223938000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:223937000-223938200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:223937000-223938200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:223937000-223938200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:223937000-223938200	Weak transcription	Brain Angular Gyrus	brain
20	chr1:223937000-223938200	Weak transcription	Ovary	ovary
21	chr1:223937000-223938200	Weak transcription	Pancreas	Pancrea
22	chr1:223937000-223938200	Weak transcription	Psoas Muscle	Psoas
23	chr1:223937000-223938400	Weak transcription	Aorta	Aorta
24	chr1:223937000-223938400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:223937000-223938400	Weak transcription	HepG2	liver
26	chr1:223937000-223939000	Weak transcription	Liver	Liver
27	chr1:223937000-223939000	Weak transcription	Fetal Thymus	thymus
28	chr1:223937000-223939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:223937000-223939600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:223937000-223940000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:223937000-223940200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:223937000-223940200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:223937000-223940200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:223937000-223940200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:223937000-223940200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:223937000-223940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:223937000-223940400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:223937000-223940600	Weak transcription	Small Intestine	intestine
39	chr1:223937000-223940800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:223937000-223943200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:223937000-223943400	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr1:223937000-223945400	Strong transcription	Hela-S3	cervix
43	chr1:223937000-223947600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:223937000-223948000	Strong transcription	Lung	lung
45	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
46	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
48	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
49	chr1:223937000-223954400	Strong transcription	Gastric	stomach
50	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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