Variant report

Variant	rs12464877
Chromosome Location	chr2:55327550-55327551
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55276735..55279463-chr2:55327258..55330571,3	K562	blood:
2	chr2:55323307..55326609-chr2:55326695..55329491,3	K562	blood:
3	chr2:55312676..55314647-chr2:55325733..55328474,2	K562	blood:
4	chr2:55325626..55328074-chr2:55345685..55348277,2	K562	blood:
5	chr2:55327279..55331330-chr2:55337574..55341174,5	K562	blood:
6	chr2:55323175..55325737-chr2:55325839..55328414,2	MCF-7	breast:
7	chr2:55326388..55330538-chr2:55335061..55337994,3	K562	blood:
8	chr2:55326463..55328844-chr2:55338475..55342420,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266376	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12464796	0.87[GIH][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes]
rs12990261	0.82[AMR][1000 genomes]
rs17046514	1.00[ASW][hapmap]
rs2580768	1.00[ASW][hapmap]
rs2580770	1.00[ASW][hapmap]
rs2580771	1.00[ASW][hapmap]
rs2588515	1.00[ASW][hapmap]
rs2968778	0.91[CEU][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35275603	0.82[AMR][1000 genomes]
rs4671993	1.00[ASW][hapmap]
rs4672003	1.00[ASW][hapmap]
rs4672018	1.00[ASW][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6718269	0.82[AMR][1000 genomes]
rs6734314	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006172	chr2:55322883-55340812	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2760568	chr2:55322895-55330350	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv2763510	chr2:55322895-55330350	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3345871	chr2:55323717-55336931	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3457756	chr2:55323755-55336917	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3457755	chr2:55323788-55336864	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3457757	chr2:55323788-55336864	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv9883	chr2:55323841-55336774	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv999212	chr2:55324276-55340812	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv2421886	chr2:55324288-55335045	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv3693301	chr2:55324960-55335045	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv517331	chr2:55324960-55335045	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv817951	chr2:55324960-55335045	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv438350	chr2:55327091-55333235	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55318400-55329600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:55321600-55339400	Weak transcription	Thymus	Thymus
3	chr2:55321800-55336400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:55322600-55327800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:55323600-55328200	Enhancers	K562	blood
6	chr2:55323600-55330000	Enhancers	HSMM	muscle
7	chr2:55323800-55327800	Enhancers	Brain Hippocampus Middle	brain
8	chr2:55323800-55329800	Enhancers	NH-A	brain
9	chr2:55324800-55327600	Weak transcription	Placenta	Placenta
10	chr2:55325200-55340400	Weak transcription	Gastric	stomach
11	chr2:55325400-55330400	Weak transcription	Fetal Intestine Small	intestine
12	chr2:55326000-55328000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:55326200-55328400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr2:55326400-55327800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:55326400-55328000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:55326400-55328000	Enhancers	Fetal Heart	heart
17	chr2:55326400-55328000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:55326600-55327600	Enhancers	HMEC	breast
19	chr2:55326600-55327800	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:55326600-55327800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr2:55326600-55327800	Enhancers	Fetal Stomach	stomach
22	chr2:55326600-55327800	Enhancers	Ovary	ovary
23	chr2:55326600-55327800	Enhancers	Stomach Mucosa	stomach
24	chr2:55326600-55328000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:55326600-55328000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr2:55326600-55329600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:55326600-55329600	Enhancers	NHEK	skin
28	chr2:55326600-55330000	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:55326800-55327600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr2:55326800-55327600	Enhancers	Small Intestine	intestine
31	chr2:55326800-55327800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:55326800-55327800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:55326800-55328000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr2:55326800-55330600	Enhancers	Stomach Smooth Muscle	stomach
35	chr2:55326800-55334600	Weak transcription	Brain Angular Gyrus	brain
36	chr2:55327000-55327600	Enhancers	HepG2	liver
37	chr2:55327000-55327800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:55327000-55327800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:55327000-55327800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr2:55327000-55328000	Enhancers	Brain Substantia Nigra	brain
41	chr2:55327000-55328000	Enhancers	Fetal Lung	lung
42	chr2:55327000-55328200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr2:55327000-55330800	Enhancers	Colon Smooth Muscle	Colon
44	chr2:55327200-55327600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr2:55327200-55327600	Flanking Active TSS	Right Atrium	heart
46	chr2:55327200-55327800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:55327200-55327800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:55327200-55327800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:55327200-55327800	Enhancers	Aorta	Aorta
50	chr2:55327200-55327800	Enhancers	Fetal Muscle Leg	muscle

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