Variant report

Variant	rs74089565
Chromosome Location	chr12:49955339-49955340
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	chr12:49954898-49955352	K562	blood:	n/a	n/a
2	POLR2A	chr12:49954915-49955408	K562	blood:	n/a	n/a
3	POLR2A	chr12:49954932-49955383	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49930852..49937653-chr12:49953841..49959391,7	K562	blood:
2	chr12:49759499..49761453-chr12:49953026..49955590,2	MCF-7	breast:
3	chr12:49954419..49956217-chr12:50016966..50019310,2	MCF-7	breast:

Variant related genes	Relation type
MCRS1	TF binding region
ENSG00000135519	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17853062	1.00[AMR][1000 genomes]
rs56005192	1.00[AMR][1000 genomes]
rs56014465	1.00[AMR][1000 genomes]
rs56140046	1.00[AMR][1000 genomes]
rs56330550	1.00[AMR][1000 genomes]
rs57546911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60865902	1.00[AMR][1000 genomes]
rs61110708	1.00[AMR][1000 genomes]
rs7309243	1.00[AMR][1000 genomes]
rs74087114	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74087152	1.00[AMR][1000 genomes]
rs74087193	1.00[AMR][1000 genomes]
rs74089028	1.00[AMR][1000 genomes]
rs74089030	1.00[AMR][1000 genomes]
rs74089031	1.00[AMR][1000 genomes]
rs74089060	1.00[AMR][1000 genomes]
rs74089561	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089572	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49943200-49959600	Weak transcription	Right Atrium	heart
2	chr12:49946000-49960200	Weak transcription	Fetal Brain Male	brain
3	chr12:49946200-49955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:49947200-49956000	Weak transcription	Fetal Heart	heart
5	chr12:49948200-49960400	Strong transcription	Fetal Brain Female	brain
6	chr12:49948200-49960400	Strong transcription	Fetal Intestine Small	intestine
7	chr12:49949200-49960400	Strong transcription	Fetal Stomach	stomach
8	chr12:49949400-49957000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:49949400-49957600	Strong transcription	Right Ventricle	heart
10	chr12:49949400-49958000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:49949400-49958200	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:49949400-49958200	Strong transcription	Brain Anterior Caudate	brain
13	chr12:49949400-49958600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:49949400-49959000	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr12:49949400-49959200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:49949400-49959200	Strong transcription	Gastric	stomach
17	chr12:49949400-49959400	Strong transcription	Brain Germinal Matrix	brain
18	chr12:49949400-49959800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:49949400-49959800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:49949400-49960000	Strong transcription	Thymus	Thymus
21	chr12:49949400-49960200	Strong transcription	NHLF	lung
22	chr12:49949600-49955600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:49949600-49956600	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:49949600-49958000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:49949600-49958000	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:49949600-49958200	Strong transcription	Fetal Thymus	thymus
27	chr12:49949600-49958400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr12:49949600-49959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:49949600-49959600	Strong transcription	Placenta	Placenta
30	chr12:49949600-49959600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:49949600-49959800	Strong transcription	Brain Hippocampus Middle	brain
32	chr12:49949600-49960000	Strong transcription	Fetal Intestine Large	intestine
33	chr12:49949600-49960400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:49949600-49960400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:49949800-49957000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:49949800-49957200	Strong transcription	Esophagus	oesophagus
37	chr12:49949800-49957400	Strong transcription	Primary T cells from cord blood	blood
38	chr12:49949800-49957600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:49949800-49958000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:49949800-49958000	Strong transcription	Brain Angular Gyrus	brain
41	chr12:49949800-49958200	Strong transcription	Left Ventricle	heart
42	chr12:49949800-49958400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:49949800-49959000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:49949800-49959400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:49949800-49959600	Strong transcription	Fetal Lung	lung
46	chr12:49949800-49959600	Strong transcription	Pancreas	Pancrea
47	chr12:49949800-49959600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr12:49949800-49959600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:49949800-49959600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr12:49949800-49959800	Strong transcription	Primary monocytes fromperipheralblood	blood

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