Variant report

Variant	rs34369
Chromosome Location	chr12:9393573-9393574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:9393569-9393601	NB4	blood:	n/a	n/a

Variant related genes	Relation type
PTMAP4	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2195209	0.82[EUR][1000 genomes]
rs2195211	0.85[EUR][1000 genomes]
rs34363	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs34364	0.87[EUR][1000 genomes]
rs34370	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4883222	0.81[EUR][1000 genomes]
rs7301988	0.82[EUR][1000 genomes]
rs7959360	0.81[EUR][1000 genomes]
rs7979115	0.91[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs972110	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
7	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
8	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
10	nsv1048917	chr12:9393282-9436132	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34369	CDCA3	cis	parietal	SCAN
rs34369	CLEC4D	cis	cerebellum	SCAN
rs34369	CLEC2D	cis	cerebellum	SCAN
rs34369	RBP5	cis	cerebellum	SCAN
rs34369	RPL13P5	cis	parietal	SCAN
rs34369	CREBL2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9392600-9393600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr12:9392600-9393600	Active TSS	Primary hematopoietic stem cells	blood
3	chr12:9392600-9393600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:9392600-9393600	Active TSS	Aorta	Aorta
5	chr12:9392600-9393600	Active TSS	Brain Angular Gyrus	brain
6	chr12:9392600-9393600	Active TSS	Brain Anterior Caudate	brain
7	chr12:9392600-9393600	Active TSS	Rectal Smooth Muscle	rectum
8	chr12:9392600-9393800	Active TSS	Adipose Nuclei	Adipose
9	chr12:9392600-9393800	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr12:9392600-9393800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr12:9392600-9393800	Active TSS	Left Ventricle	heart
12	chr12:9392600-9393800	Active TSS	Right Atrium	heart
13	chr12:9392600-9393800	Active TSS	Stomach Smooth Muscle	stomach
14	chr12:9392600-9394000	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr12:9392600-9394200	Active TSS	Brain Cingulate Gyrus	brain
16	chr12:9392800-9393800	Active TSS	Brain Hippocampus Middle	brain
17	chr12:9392800-9393800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:9393200-9393600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr12:9393200-9393600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr12:9393200-9395400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:9393200-9395800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:9393200-9396800	Weak transcription	Psoas Muscle	Psoas
23	chr12:9393200-9397400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:9393200-9397400	Weak transcription	Pancreas	Pancrea
25	chr12:9393200-9397400	Weak transcription	Right Ventricle	heart
26	chr12:9393400-9393600	Enhancers	Primary B cells from peripheral blood	blood
27	chr12:9393400-9393600	Bivalent Enhancer	Primary T cells from cord blood	blood
28	chr12:9393400-9393600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr12:9393400-9393600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:9393400-9393600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr12:9393400-9393600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
32	chr12:9393400-9393600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:9393400-9393600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:9393400-9393600	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr12:9393400-9393600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr12:9393400-9393600	Flanking Active TSS	Fetal Brain Male	brain
37	chr12:9393400-9393600	Bivalent Enhancer	Fetal Kidney	kidney
38	chr12:9393400-9393600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
39	chr12:9393400-9393600	Enhancers	Fetal Thymus	thymus
40	chr12:9393400-9393600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
41	chr12:9393400-9393800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:9393400-9393800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr12:9393400-9393800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:9393400-9393800	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr12:9393400-9393800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr12:9393400-9393800	Flanking Active TSS	Liver	Liver
47	chr12:9393400-9393800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr12:9393400-9394000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:9393400-9394000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:9393400-9397400	Weak transcription	HMEC	breast

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