Variant report

Variant	rs62179066
Chromosome Location	chr2:180131509-180131510
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:
2	chr2:180129872..180132234-chr2:180132866..180134594,2	K562	blood:

Variant related genes	Relation type
ENSG00000237477	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12622222	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17363057	1.00[AFR][1000 genomes]
rs17454087	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17454199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17454527	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62175447	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62175448	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62175449	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62175450	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62177277	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62177280	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62177281	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62177283	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62177285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62177287	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62177289	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62177291	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62177326	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62177327	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62177328	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62177330	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62177332	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177335	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177336	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177337	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177338	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62177339	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62179067	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62179068	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62179069	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180129800-180132000	Enhancers	Fetal Heart	heart
2	chr2:180130000-180132600	Weak transcription	Placenta	Placenta
3	chr2:180130000-180132800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:180130000-180133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:180130000-180135200	Weak transcription	Brain Angular Gyrus	brain
6	chr2:180130000-180137200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:180130000-180138000	Weak transcription	Gastric	stomach
8	chr2:180130000-180138200	Weak transcription	Aorta	Aorta
9	chr2:180130000-180141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:180130000-180141200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:180130200-180131800	Enhancers	HepG2	liver
12	chr2:180130200-180132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:180130200-180132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:180130200-180133000	Weak transcription	A549	lung
18	chr2:180130200-180133000	Weak transcription	NHDF-Ad	bronchial
19	chr2:180130200-180133200	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:180130200-180136200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:180130200-180137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:180130200-180137200	Weak transcription	NH-A	brain
23	chr2:180130400-180132600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:180130400-180132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:180130400-180132600	Weak transcription	GM12878-XiMat	blood
26	chr2:180130400-180132600	Weak transcription	NHEK	skin
27	chr2:180130400-180132800	Weak transcription	HMEC	breast
28	chr2:180130400-180132800	Weak transcription	HUVEC	blood vessel
29	chr2:180130400-180133000	Weak transcription	Brain Substantia Nigra	brain
30	chr2:180130400-180133200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:180130400-180136000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:180130400-180137400	Weak transcription	Fetal Intestine Large	intestine
33	chr2:180130400-180138400	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:180130400-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:180130600-180132600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:180130600-180132800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:180130600-180133000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:180130600-180138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:180130800-180132600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:180130800-180132600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr2:180130800-180132800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:180130800-180132800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:180130800-180132800	Weak transcription	Osteobl	bone
44	chr2:180130800-180133000	Weak transcription	Adipose Nuclei	Adipose
45	chr2:180130800-180133200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:180130800-180135400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:180131000-180132200	Weak transcription	Hela-S3	cervix
48	chr2:180131000-180132800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:180131000-180132800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:180131000-180133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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