Variant report

Variant	rs2289747
Chromosome Location	chr2:55198385-55198386
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55190781..55193657-chr2:55198367..55200199,2	K562	blood:
2	chr2:55198243..55200430-chr2:55275521..55278393,2	MCF-7	breast:
3	chr2:55195869..55197384-chr2:55197903..55200472,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RTN4-1	chr2:55196736-55198803	ENSG00000248316

Variant related genes	Relation type
ENSG00000214595	Chromatin interaction
ENSG00000115310	Chromatin interaction

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

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

rs_ID	r²[population]
rs12464447	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12475787	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12475904	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17046570	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17046594	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17347089	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17418675	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2241959	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2289748	0.82[ASN][1000 genomes]
rs55659423	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55698303	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55993793	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56013263	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs67156582	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72795431	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs887	0.84[AMR][1000 genomes];0.97[EUR][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55173200-55203400	Weak transcription	Gastric	stomach
2	chr2:55181600-55203400	Weak transcription	Ovary	ovary
3	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
4	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55190000-55198400	Weak transcription	Colonic Mucosa	Colon
6	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
7	chr2:55191200-55199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:55191800-55203600	Weak transcription	Fetal Lung	lung
9	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:55192200-55198600	Strong transcription	Fetal Stomach	stomach
12	chr2:55192600-55198600	Strong transcription	Fetal Intestine Small	intestine
13	chr2:55193400-55199000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:55193400-55201800	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr2:55193400-55214800	Strong transcription	HepG2	liver
16	chr2:55193600-55200800	Strong transcription	A549	lung
17	chr2:55193600-55201800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:55193800-55198600	Genic enhancers	Lung	lung
20	chr2:55193800-55202400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:55194000-55198600	Strong transcription	Brain Germinal Matrix	brain
23	chr2:55194000-55199000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:55194200-55198600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:55194200-55204400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:55194400-55200200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:55194400-55200200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:55194400-55201400	Strong transcription	Primary B cells from cord blood	blood
30	chr2:55194600-55202200	Strong transcription	NHDF-Ad	bronchial
31	chr2:55194600-55204400	Strong transcription	Primary T cells from cord blood	blood
32	chr2:55194800-55201200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:55194800-55202400	Strong transcription	NHLF	lung
34	chr2:55195000-55199600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:55195000-55203200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:55195000-55215200	Strong transcription	Dnd41	blood
37	chr2:55195200-55199200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:55195200-55201200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:55195200-55201600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:55195200-55202000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:55195200-55202600	Strong transcription	Osteobl	bone
42	chr2:55195200-55205600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:55195200-55205800	Strong transcription	HMEC	breast
44	chr2:55195400-55198600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:55195400-55199400	Strong transcription	Fetal Intestine Large	intestine
46	chr2:55195400-55202200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:55195400-55205200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:55195600-55198400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:55195800-55198600	Genic enhancers	Brain Inferior Temporal Lobe	brain

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