Variant report

Variant	rs11608669
Chromosome Location	chr12:104917348-104917349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104913735..104915662-chr12:104916731..104918448,2	K562	blood:
2	chr12:104849686..104852352-chr12:104916410..104918510,2	K562	blood:
3	chr12:104907056..104912149-chr12:104913273..104918297,6	K562	blood:
4	chr12:104909660..104911855-chr12:104915030..104918297,3	K562	blood:
5	chr12:104908202..104911501-chr12:104915065..104918852,3	MCF-7	breast:
6	chr12:104849686..104853120-chr12:104916879..104918907,3	K562	blood:

Variant related genes	Relation type
ENSG00000258111	Chromatin interaction
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11609491	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611979	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs17035663	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1882494	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2141855	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141856	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141859	0.81[CEU][hapmap]
rs4536299	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55778791	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020814	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56138293	0.85[ASN][1000 genomes]
rs57525859	0.85[ASN][1000 genomes]
rs60351248	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7970489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972097	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7972201	1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11608669	GOLGA2B	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104901200-104919200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:104901800-104920400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:104904400-104917600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:104906800-104917600	Weak transcription	HSMM	muscle
5	chr12:104908600-104920600	Weak transcription	Right Ventricle	heart
6	chr12:104909400-104919200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:104909400-104919400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:104909800-104919400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:104910400-104918200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:104911000-104921800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:104911400-104918600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:104912000-104919200	Enhancers	Primary B cells from peripheral blood	blood
13	chr12:104912400-104918400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:104912800-104919200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:104913200-104917800	Enhancers	Right Atrium	heart
16	chr12:104913200-104918600	Enhancers	Placenta	Placenta
17	chr12:104913400-104918600	Enhancers	Spleen	Spleen
18	chr12:104913600-104919600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:104914000-104918600	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:104914000-104921200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:104914400-104918200	Enhancers	NHDF-Ad	bronchial
22	chr12:104914400-104919400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:104914600-104920400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:104914800-104917600	Weak transcription	Aorta	Aorta
25	chr12:104914800-104919600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:104914800-104919600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:104914800-104920200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:104915000-104918200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:104915200-104918200	Enhancers	HUVEC	blood vessel
30	chr12:104915200-104918200	Enhancers	Osteobl	bone
31	chr12:104915200-104918400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:104915200-104919800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:104915400-104918800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr12:104915400-104920200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:104915600-104917600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:104915600-104917800	Enhancers	Dnd41	blood
37	chr12:104915600-104918200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr12:104915600-104918400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:104915600-104918400	Enhancers	Fetal Brain Female	brain
40	chr12:104915600-104919600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:104915600-104920000	Weak transcription	Brain Germinal Matrix	brain
42	chr12:104915600-104936600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:104915800-104918000	Weak transcription	Brain Substantia Nigra	brain
44	chr12:104915800-104920200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:104916200-104918200	Enhancers	Fetal Thymus	thymus
46	chr12:104916200-104918400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr12:104916200-104918600	Enhancers	Fetal Brain Male	brain
48	chr12:104916400-104918200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr12:104916400-104918600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:104916400-104918600	Enhancers	Left Ventricle	heart

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