Variant report

Variant	rs2255026
Chromosome Location	chr2:55201038-55201039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55198988..55201900-chr2:55213351..55214997,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf63-3	chr2:55200699-55201155	NONHSAT070753
2	lnc-C2orf63-3	chr2:55200957-55201327	NONHSAT070754

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1012603	0.83[AFR][1000 genomes]
rs13031431	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17046514	0.83[AFR][1000 genomes]
rs17046579	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17046586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17046589	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17046643	0.83[AFR][1000 genomes]
rs1822617	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2241958	0.83[AFR][1000 genomes]
rs2255393	0.85[CHB][hapmap]
rs2580768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2580769	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2580770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2580771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2588513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2588515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2588516	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2588522	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2919126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2968788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972063	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34352825	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34378852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34928331	0.89[ASN][1000 genomes]
rs35981204	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4672003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672006	0.83[AFR][1000 genomes]
rs4672009	0.83[AFR][1000 genomes]
rs57737203	0.83[AFR][1000 genomes]
rs60553807	0.83[AFR][1000 genomes]
rs6545464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6734314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739210	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72795434	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7355716	0.84[CHB][hapmap]

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:125 , 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	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
6	chr2:55191800-55203600	Weak transcription	Fetal Lung	lung
7	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:55193400-55201800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr2:55193400-55214800	Strong transcription	HepG2	liver
11	chr2:55193600-55201800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:55193800-55202400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:55194200-55204400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:55194400-55201400	Strong transcription	Primary B cells from cord blood	blood
18	chr2:55194600-55202200	Strong transcription	NHDF-Ad	bronchial
19	chr2:55194600-55204400	Strong transcription	Primary T cells from cord blood	blood
20	chr2:55194800-55201200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:55194800-55202400	Strong transcription	NHLF	lung
22	chr2:55195000-55203200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:55195000-55215200	Strong transcription	Dnd41	blood
24	chr2:55195200-55201200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:55195200-55201600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:55195200-55202000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:55195200-55202600	Strong transcription	Osteobl	bone
28	chr2:55195200-55205600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:55195200-55205800	Strong transcription	HMEC	breast
30	chr2:55195400-55202200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55195400-55205200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:55196000-55202200	Strong transcription	NH-A	brain
35	chr2:55196000-55203400	Weak transcription	Pancreas	Pancrea
36	chr2:55196000-55205800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:55196200-55202600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:55196200-55202600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:55196200-55203400	Weak transcription	Right Atrium	heart
40	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
42	chr2:55196400-55201200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:55196600-55208400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:55196800-55201200	Strong transcription	HSMM	muscle
47	chr2:55196800-55203400	Strong transcription	Fetal Thymus	thymus
48	chr2:55196800-55203800	Strong transcription	HUVEC	blood vessel
49	chr2:55196800-55204600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr2:55196800-55204800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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