Variant report

Variant	rs2588515
Chromosome Location	chr2:55210856-55210857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1012603	0.83[AFR][1000 genomes]
rs12464877	1.00[ASW][hapmap]
rs13031431	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17046514	1.00[ASW][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs17046579	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17046586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17046589	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17046643	0.83[AFR][1000 genomes]
rs1822617	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2241958	0.83[AFR][1000 genomes]
rs2255026	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]
rs2255393	0.85[CHB][hapmap]
rs2580768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2580769	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2580770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2580771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2588513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2588516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588522	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2919126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972063	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34352825	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34378852	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34928331	0.94[ASN][1000 genomes]
rs35981204	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671993	1.00[ASW][hapmap]
rs4672003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672006	0.83[AFR][1000 genomes]
rs4672009	0.83[AFR][1000 genomes]
rs4672018	1.00[ASW][hapmap]
rs57737203	0.83[AFR][1000 genomes]
rs60553807	0.83[AFR][1000 genomes]
rs6545464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6734314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739210	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72795434	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2588515	CCDC88A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55193400-55214800	Strong transcription	HepG2	liver
5	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:55195000-55215200	Strong transcription	Dnd41	blood
9	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
12	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:55198200-55212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:55198600-55215200	Weak transcription	Lung	lung
17	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:55199200-55212400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
20	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
21	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
22	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
23	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
24	chr2:55204200-55214800	Strong transcription	Fetal Thymus	thymus
25	chr2:55204800-55211600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:55205000-55211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:55205200-55213400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:55205200-55213600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:55205200-55214600	Strong transcription	Fetal Muscle Leg	muscle
30	chr2:55205200-55214600	Weak transcription	Right Atrium	heart
31	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
32	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
33	chr2:55205600-55211000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:55205600-55214800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:55205800-55211800	Weak transcription	Fetal Stomach	stomach
36	chr2:55205800-55216000	Weak transcription	Fetal Intestine Small	intestine
37	chr2:55206200-55213000	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:55206400-55214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:55206600-55214000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:55206600-55214800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:55206600-55215200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:55206800-55213800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:55206800-55214800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:55207200-55212800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:55207200-55213200	Weak transcription	Fetal Brain Female	brain
46	chr2:55207600-55211200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:55207600-55214800	Strong transcription	K562	blood
48	chr2:55207600-55215200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:55207800-55213400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:55207800-55214800	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links