Variant report

Variant	rs12733939
Chromosome Location	chr1:171455279-171455280
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171449334..171452754-chr1:171452810..171456877,5	K562	blood:
2	chr1:171387474..171389314-chr1:171452671..171455451,2	MCF-7	breast:
3	chr1:171454646..171455442-chr6:34360140..34360662,2	HCT-116	colon:
4	chr1:171405355..171408089-chr1:171454758..171456497,2	MCF-7	breast:
5	chr1:171453211..171456610-chr1:171708836..171712780,4	K562	blood:
6	chr1:171449410..171451511-chr1:171453744..171456150,2	MCF-7	breast:
7	chr1:171454462..171455380-chr16:31483667..31484585,2	Hela-S3	cervix:
8	chr1:171454548..171455485-chr5:217985..218553,2	Hela-S3	cervix:
9	chr1:171454829..171458429-chr1:171468344..171472224,4	MCF-7	breast:
10	chr1:171454625..171455402-chr3:53381284..53382126,2	Hela-S3	cervix:
11	chr1:171453426..171457241-chr1:171461305..171463614,3	MCF-7	breast:
12	chr1:171455198..171457522-chr1:171482757..171484309,2	MCF-7	breast:
13	chr1:171454832..171457416-chr1:171532662..171535516,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140682	Chromatin interaction
ENSG00000164366	Chromatin interaction
ENSG00000073578	Chromatin interaction
ENSG00000272325	Chromatin interaction
ENSG00000202082	Chromatin interaction
ENSG00000238859	Chromatin interaction
ENSG00000239373	Chromatin interaction
ENSG00000162290	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1055417	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913167	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119596	0.90[ASN][1000 genomes]
rs12129856	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131694	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136576	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12137832	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139715	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12142594	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145045	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145085	0.81[EUR][1000 genomes]
rs12146022	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12734261	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12759907	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294292	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294293	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235471	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235472	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235488	0.83[EUR][1000 genomes]
rs235495	0.83[EUR][1000 genomes]
rs235498	0.83[EUR][1000 genomes]
rs235502	0.83[EUR][1000 genomes]
rs235507	0.83[EUR][1000 genomes]
rs235886	0.82[EUR][1000 genomes]
rs235892	0.80[EUR][1000 genomes]
rs235895	0.80[EUR][1000 genomes]
rs235910	0.83[EUR][1000 genomes]
rs235911	0.80[EUR][1000 genomes]
rs235912	0.83[EUR][1000 genomes]
rs56207586	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71637410	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71637418	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71637419	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74122850	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534464	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7534557	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7538745	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171453200-171455800	Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:171453600-171455400	Active TSS	Primary hematopoietic stem cells	blood
3	chr1:171453600-171455600	Active TSS	Adipose Nuclei	Adipose
4	chr1:171453600-171455600	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:171453600-171455600	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr1:171453600-171456000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:171453600-171456000	Active TSS	A549	lung
8	chr1:171453600-171456200	Active TSS	NHLF	lung
9	chr1:171453600-171456400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:171453600-171457400	Active TSS	GM12878-XiMat	blood
11	chr1:171453600-171458200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:171453800-171455600	Active TSS	Brain Cingulate Gyrus	brain
13	chr1:171453800-171455600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr1:171453800-171455600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:171453800-171455600	Active TSS	Thymus	Thymus
16	chr1:171453800-171455800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:171453800-171455800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr1:171453800-171456000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:171453800-171456000	Active TSS	Muscle Satellite Cultured Cells	--
20	chr1:171453800-171456000	Active TSS	Colonic Mucosa	Colon
21	chr1:171453800-171456000	Active TSS	Fetal Kidney	kidney
22	chr1:171453800-171456000	Active TSS	Fetal Lung	lung
23	chr1:171453800-171456000	Active TSS	NH-A	brain
24	chr1:171453800-171456200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:171453800-171456200	Active TSS	HSMM	muscle
26	chr1:171453800-171456400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:171453800-171456400	Active TSS	Ovary	ovary
28	chr1:171453800-171456400	Active TSS	HSMMtube	muscle
29	chr1:171453800-171456600	Active TSS	Psoas Muscle	Psoas
30	chr1:171453800-171456600	Active TSS	Right Ventricle	heart
31	chr1:171453800-171457600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:171454000-171455400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:171454000-171455400	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr1:171454000-171455400	Active TSS	Duodenum Mucosa	Duodenum
35	chr1:171454000-171455400	Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:171454000-171455600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:171454000-171455600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:171454000-171455600	Active TSS	Primary monocytes fromperipheralblood	blood
39	chr1:171454000-171455600	Active TSS	Primary T cells fromperipheralblood	blood
40	chr1:171454000-171455600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:171454000-171455600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:171454000-171455600	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr1:171454000-171455600	Active TSS	Liver	Liver
44	chr1:171454000-171455600	Active TSS	Brain Anterior Caudate	brain
45	chr1:171454000-171455600	Active TSS	Colon Smooth Muscle	Colon
46	chr1:171454000-171455600	Active TSS	Fetal Brain Female	brain
47	chr1:171454000-171455600	Active TSS	Fetal Muscle Leg	muscle
48	chr1:171454000-171455600	Active TSS	Osteobl	bone
49	chr1:171454000-171455800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:171454000-171455800	Active TSS	Brain Hippocampus Middle	brain

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