Variant report

Variant	rs12119779
Chromosome Location	chr1:212559906-212559907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212559670..212562304-chr1:212569400..212571450,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1056985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863955	0.93[CEU][hapmap]
rs10863965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119886	0.93[CEU][hapmap]
rs11119891	1.00[CEU][hapmap]
rs11119907	0.82[EUR][1000 genomes]
rs11119908	0.82[EUR][1000 genomes]
rs11119910	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11119918	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11119927	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119934	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119937	0.83[AFR][1000 genomes]
rs12031941	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12033979	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118709	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12128123	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12128965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs12129267	0.82[EUR][1000 genomes]
rs12133582	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133636	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs12134599	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12136095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12137798	0.82[EUR][1000 genomes]
rs12138533	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140158	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12141427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143853	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12145170	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12145377	0.92[CEU][hapmap]
rs12145484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12239580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12403586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12561785	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1342152	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1388033	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1388034	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs14123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17018777	0.93[CEU][hapmap]
rs17018847	1.00[CEU][hapmap]
rs17018853	1.00[CEU][hapmap]
rs17666015	0.83[EUR][1000 genomes]
rs1808986	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2298115	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs3754142	0.83[CHB][hapmap]
rs3754144	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3767867	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3767868	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3767872	1.00[AFR][1000 genomes]
rs3820513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4338424	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4548507	1.00[ASN][1000 genomes]
rs4951596	0.87[ASN][1000 genomes]
rs4951597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59001230	1.00[AFR][1000 genomes]
rs74138154	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs765364	0.82[JPT][hapmap]
rs903119	1.00[CEU][hapmap]

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	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12119779	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
4	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
5	chr1:212529400-212562400	Strong transcription	Dnd41	blood
6	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:212532400-212560200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:212534000-212570200	Weak transcription	HSMM	muscle
9	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:212534600-212560000	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:212535000-212561400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:212535200-212560200	Weak transcription	Hela-S3	cervix
13	chr1:212536200-212561600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:212538000-212571000	Weak transcription	NH-A	brain
15	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
16	chr1:212540600-212562600	Weak transcription	Osteobl	bone
17	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
18	chr1:212542800-212561600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
20	chr1:212545000-212561000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:212546800-212560200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:212546800-212560400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:212547000-212562600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:212547000-212563400	Strong transcription	Fetal Thymus	thymus
25	chr1:212547200-212561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:212547400-212562400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:212547400-212562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:212548200-212560600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:212548600-212563800	Strong transcription	Primary T cells from cord blood	blood
30	chr1:212549400-212560600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:212549400-212561000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:212549600-212560200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:212550400-212561000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:212550400-212562800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:212551400-212561800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:212551600-212560000	Weak transcription	Colonic Mucosa	Colon
37	chr1:212552000-212562000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:212553000-212562600	Strong transcription	GM12878-XiMat	blood
39	chr1:212553200-212562000	Weak transcription	Liver	Liver
40	chr1:212553200-212569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:212553200-212578400	Weak transcription	K562	blood
42	chr1:212553400-212560200	Weak transcription	Right Ventricle	heart
43	chr1:212554600-212560600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:212554600-212560600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:212554600-212562400	Strong transcription	Thymus	Thymus
46	chr1:212554800-212560600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:212554800-212562400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:212554800-212562600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:212555000-212560600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:212555000-212560600	Strong transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links