Variant report

Variant	rs1532587
Chromosome Location	chr12:106700709-106700710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:106695130-106701174	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:106695562..106697778-chr12:106698885..106700984,2	K562	blood:
2	chr12:106699658..106703217-chr12:106715464..106718828,3	K562	blood:
3	chr12:106640546..106642318-chr12:106700436..106703373,2	MCF-7	breast:
4	chr12:106700481..106701223-chr12:106710836..106711809,2	K562	blood:
5	chr12:106700302..106702349-chr12:106702837..106704889,2	K562	blood:
6	chr12:106693434..106696954-chr12:106697519..106701215,4	MCF-7	breast:
7	chr12:106699381..106702338-chr12:106750472..106752773,2	MCF-7	breast:
8	chr12:106699658..106701808-chr12:106715464..106717408,2	K562	blood:

No data

Variant related genes	Relation type
CKAP4	TF binding region
ENSG00000166046	Chromatin interaction
ENSG00000013503	Chromatin interaction
ENSG00000136026	Chromatin interaction
ENSG00000258355	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10861572	0.96[ASN][1000 genomes]
rs10861574	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861575	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112931	0.95[ASN][1000 genomes]
rs2077730	0.85[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2249837	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2250108	0.85[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2250705	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2250708	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2250709	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2250713	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250936	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264757	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264762	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2264814	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2264815	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2264816	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2279759	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs2465356	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35816179	0.96[ASN][1000 genomes]
rs36139467	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314289	0.96[ASN][1000 genomes]
rs904614	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1532587	NUAK1	cis	cerebellum	SCAN
rs1532587	TCP11L2	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106697200-106702600	Enhancers	Fetal Heart	heart
2	chr12:106697800-106701200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:106697800-106702800	Weak transcription	NHEK	skin
4	chr12:106697800-106703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:106697800-106703600	Enhancers	Fetal Intestine Large	intestine
6	chr12:106698000-106702200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:106698000-106702200	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr12:106698000-106702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:106698000-106702600	Weak transcription	HSMM	muscle
10	chr12:106698000-106703000	Weak transcription	NHLF	lung
11	chr12:106698000-106704000	Weak transcription	GM12878-XiMat	blood
12	chr12:106698000-106705600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr12:106698000-106708400	Weak transcription	Small Intestine	intestine
14	chr12:106698000-106709000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:106698200-106701000	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:106698200-106701600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:106698200-106701800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:106698200-106702600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:106698200-106702600	Weak transcription	HMEC	breast
20	chr12:106698200-106702800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:106698200-106702800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:106698200-106702800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:106698200-106702800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:106698200-106702800	Weak transcription	Spleen	Spleen
25	chr12:106698200-106703000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:106698200-106703200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:106698200-106703200	Weak transcription	Osteobl	bone
28	chr12:106698200-106703800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:106698200-106703800	Weak transcription	Fetal Stomach	stomach
30	chr12:106698200-106704200	Enhancers	Colon Smooth Muscle	Colon
31	chr12:106698200-106706000	Weak transcription	Placenta	Placenta
32	chr12:106698200-106708000	Weak transcription	Liver	Liver
33	chr12:106698400-106701000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:106698400-106702200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr12:106698400-106702400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:106698400-106703200	Weak transcription	NHDF-Ad	bronchial
37	chr12:106698400-106708000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:106698400-106709800	Weak transcription	Fetal Lung	lung
39	chr12:106698600-106701000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:106698600-106701000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:106698600-106701600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:106698600-106702600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:106698600-106709600	Weak transcription	Brain Germinal Matrix	brain
44	chr12:106698800-106701000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:106698800-106702000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:106698800-106702000	Weak transcription	HSMMtube	muscle
47	chr12:106698800-106702200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:106698800-106705400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr12:106698800-106708400	Weak transcription	Thymus	Thymus
50	chr12:106698800-106709200	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links