Variant report

Variant	rs17123827
Chromosome Location	chr12:49992283-49992284
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	POLR2A	chr12:49992038-49992574	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:49992236-49992836	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49991394..49993923-chr12:50016054..50019750,3	MCF-7	breast:
2	chr12:49758663..49761536-chr12:49989987..49992375,3	K562	blood:

Variant related genes	Relation type
PRPF40B	TF binding region
ENSG00000110844	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10128824	1.00[AMR][1000 genomes]
rs11169110	1.00[AMR][1000 genomes]
rs11169114	1.00[AMR][1000 genomes]
rs11169115	1.00[AMR][1000 genomes]
rs11169120	1.00[AMR][1000 genomes]
rs11169123	1.00[AMR][1000 genomes]
rs11609068	0.86[YRI][hapmap]
rs12297814	1.00[AMR][1000 genomes]
rs12299477	1.00[AMR][1000 genomes]
rs12299666	1.00[AMR][1000 genomes]
rs12299743	1.00[AMR][1000 genomes]
rs12299751	1.00[AMR][1000 genomes]
rs12300376	1.00[YRI][hapmap]
rs12300962	1.00[AMR][1000 genomes]
rs12306951	1.00[AMR][1000 genomes]
rs12310580	1.00[AMR][1000 genomes]
rs12312112	1.00[AMR][1000 genomes]
rs12313657	1.00[AMR][1000 genomes]
rs12313681	1.00[AMR][1000 genomes]
rs12314036	1.00[AMR][1000 genomes]
rs12315508	1.00[AMR][1000 genomes]
rs12317162	1.00[AMR][1000 genomes]
rs12319527	1.00[AMR][1000 genomes]
rs12320895	1.00[AMR][1000 genomes]
rs1317263	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs17119738	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs17123724	1.00[YRI][hapmap]
rs17123778	1.00[YRI][hapmap]
rs17123787	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17123879	1.00[AMR][1000 genomes]
rs17123924	1.00[AMR][1000 genomes]
rs9804867	1.00[AMR][1000 genomes]
rs9805090	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
2	chr12:49976800-49994000	Weak transcription	Liver	Liver
3	chr12:49977600-49996200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:49978800-49994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49979600-50002600	Weak transcription	HepG2	liver
6	chr12:49979800-49995600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:49979800-49998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:49980400-50000200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:49981000-49994000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:49982200-49993600	Weak transcription	Brain Germinal Matrix	brain
11	chr12:49982200-49993800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:49982600-49993200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:49982600-50015400	Weak transcription	Pancreas	Pancrea
14	chr12:49982800-49994000	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:49982800-49996000	Weak transcription	Brain Angular Gyrus	brain
16	chr12:49983000-49993600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:49983000-49996000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:49983200-49992400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:49983200-49993600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:49983200-49993600	Weak transcription	NHLF	lung
21	chr12:49983200-49994000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:49983200-49994000	Weak transcription	Adipose Nuclei	Adipose
23	chr12:49983200-49994400	Weak transcription	Right Ventricle	heart
24	chr12:49983200-49995000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:49983200-49999400	Weak transcription	HSMMtube	muscle
26	chr12:49983200-50002800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:49983400-49992400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:49983400-49994800	Weak transcription	HSMM	muscle
29	chr12:49983400-50002800	Weak transcription	NHEK	skin
30	chr12:49985000-49994800	Weak transcription	Ovary	ovary
31	chr12:49985200-49992600	Weak transcription	GM12878-XiMat	blood
32	chr12:49985200-49993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:49985200-49998600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:49985200-49998600	Weak transcription	Placenta	Placenta
35	chr12:49985200-50003000	Weak transcription	Lung	lung
36	chr12:49985400-49993000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:49985400-49993800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:49985400-49996200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:49985400-49997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:49985400-49998000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:49985600-49993200	Weak transcription	Fetal Intestine Small	intestine
42	chr12:49985600-49993800	Weak transcription	Primary T cells from cord blood	blood
43	chr12:49985600-49993800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:49985600-49994000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:49985600-49995800	Weak transcription	Thymus	Thymus
46	chr12:49985600-49998800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:49985800-49998400	Weak transcription	Fetal Lung	lung
48	chr12:49987200-49993400	Weak transcription	Fetal Brain Female	brain
49	chr12:49987200-49998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:49990600-49998400	Weak transcription	Fetal Heart	heart

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