Variant report

Variant	rs1554259
Chromosome Location	chr2:172694629-172694630
allele	A/G
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	HDAC2	chr2:172694365-172694672	HepG2	liver:	n/a	n/a
2	CEBPB	chr2:172694219-172694645	HepG2	liver:	n/a	chr2:172694453-172694464

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172694507..172697464-chr9:100745031..100747138,2	MCF-7	breast:

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11673831	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11675404	0.80[AMR][1000 genomes]
rs11675891	0.83[AMR][1000 genomes]
rs12991441	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13016580	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13017695	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13021138	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13024662	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17427311	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17427473	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17499306	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17499502	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17848721	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1996424	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2138349	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2357062	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34108287	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34221876	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34632749	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34962243	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35162284	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3770459	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62182397	0.80[AMR][1000 genomes]
rs62184174	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72889853	0.80[EUR][1000 genomes]
rs74173119	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs979955	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172681000-172695000	Weak transcription	Pancreas	Pancrea
2	chr2:172685600-172694800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:172686200-172698800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:172689000-172696400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr2:172689400-172712200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:172689600-172695200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:172689600-172696600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:172689800-172695200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:172689800-172695400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:172689800-172696400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:172690200-172697000	Strong transcription	Primary B cells from cord blood	blood
12	chr2:172690200-172697800	Weak transcription	Fetal Stomach	stomach
13	chr2:172690200-172720600	Weak transcription	Gastric	stomach
14	chr2:172690200-172721000	Weak transcription	Aorta	Aorta
15	chr2:172690200-172750200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:172690600-172712000	Weak transcription	Hela-S3	cervix
17	chr2:172691200-172697000	Strong transcription	Dnd41	blood
18	chr2:172691200-172698800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:172691400-172695200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:172691400-172738600	Weak transcription	Esophagus	oesophagus
21	chr2:172691600-172696800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:172691800-172702000	Weak transcription	HMEC	breast
23	chr2:172692200-172714400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:172692200-172733400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:172692400-172695200	Enhancers	Osteobl	bone
26	chr2:172692600-172695200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:172693200-172696400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:172693200-172697800	Weak transcription	Lung	lung
29	chr2:172693200-172728000	Weak transcription	Colonic Mucosa	Colon
30	chr2:172693400-172695000	Enhancers	Liver	Liver
31	chr2:172693400-172697600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:172693400-172711800	Weak transcription	HSMMtube	muscle
33	chr2:172693400-172713200	Weak transcription	NH-A	brain
34	chr2:172693400-172734800	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:172693600-172700000	Weak transcription	Placenta	Placenta
36	chr2:172693600-172700000	Weak transcription	Thymus	Thymus
37	chr2:172693600-172708200	Weak transcription	Fetal Heart	heart
38	chr2:172693600-172709000	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:172693600-172712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:172693600-172712200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:172693600-172713200	Weak transcription	Fetal Brain Male	brain
42	chr2:172693600-172724200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:172693600-172734400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:172693600-172734600	Weak transcription	HSMM	muscle
45	chr2:172693800-172694800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:172693800-172694800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:172693800-172695600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:172693800-172696800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:172693800-172697400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:172693800-172697800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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