Variant report

Variant	rs62178459
Chromosome Location	chr2:133998606-133998607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10167342	0.95[EUR][1000 genomes]
rs10182118	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10193871	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206544	0.93[EUR][1000 genomes]
rs10210486	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10496702	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12464930	0.88[EUR][1000 genomes]
rs13390487	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13413333	0.95[EUR][1000 genomes]
rs13414129	0.97[ASN][1000 genomes]
rs13418981	0.91[EUR][1000 genomes]
rs13430905	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431418	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1430169	0.88[EUR][1000 genomes]
rs17800749	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1820927	0.88[EUR][1000 genomes]
rs1835341	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2115865	0.90[EUR][1000 genomes]
rs2217428	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4057049	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62179960	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62179961	0.88[EUR][1000 genomes]
rs62179967	0.88[EUR][1000 genomes]
rs62179969	0.91[EUR][1000 genomes]
rs62179970	0.91[EUR][1000 genomes]
rs6430405	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6744863	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6749561	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6756852	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7568471	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7600407	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7600871	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7603759	0.82[AMR][1000 genomes];0.94[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	nsv949629	chr2:133830379-134014961	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1001601	chr2:133838626-134005959	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011100	chr2:133900062-134046163	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1005405	chr2:133930876-134055434	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv535929	chr2:133930876-134055434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133991600-134005400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:133994000-134023600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:133997600-133999400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:133997800-133998800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:133997800-133998800	Enhancers	Fetal Stomach	stomach
6	chr2:133997800-133999200	Enhancers	Fetal Brain Female	brain
7	chr2:133997800-133999200	Enhancers	Fetal Lung	lung
8	chr2:133997800-134000400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:133998000-133998800	Enhancers	Adipose Nuclei	Adipose
10	chr2:133998000-133998800	Enhancers	Fetal Heart	heart
11	chr2:133998000-133999000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr2:133998000-133999000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:133998000-133999200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:133998000-133999200	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:133998000-133999200	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr2:133998000-133999200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:133998000-133999400	Enhancers	Liver	Liver
18	chr2:133998200-133999000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:133998200-133999200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:133998200-133999400	Active TSS	Brain Anterior Caudate	brain
21	chr2:133998400-133998800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:133998400-133998800	Active TSS	Brain Cingulate Gyrus	brain
23	chr2:133998400-133998800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:133998400-133999000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:133998400-133999000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:133998400-133999000	Active TSS	Brain Hippocampus Middle	brain
27	chr2:133998400-133999000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr2:133998400-133999000	Active TSS	Ovary	ovary
29	chr2:133998400-133999000	Active TSS	Stomach Smooth Muscle	stomach
30	chr2:133998400-133999000	Active TSS	Hela-S3	cervix
31	chr2:133998400-133999000	Active TSS	NH-A	brain
32	chr2:133998400-133999000	Active TSS	NHDF-Ad	bronchial
33	chr2:133998400-133999200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:133998400-133999200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:133998400-133999200	Active TSS	Fetal Brain Male	brain
36	chr2:133998400-133999200	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:133998400-133999200	Weak transcription	Lung	lung
38	chr2:133998400-133999400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:133998400-134005000	Weak transcription	Psoas Muscle	Psoas
40	chr2:133998400-134005800	Weak transcription	Left Ventricle	heart
41	chr2:133998600-133999000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:133998600-133999000	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr2:133998600-133999000	Flanking Active TSS	A549	lung
44	chr2:133998600-133999000	Active TSS	Osteobl	bone
45	chr2:133998600-133999200	Active TSS	NHLF	lung
46	chr2:133998600-134003800	Weak transcription	Brain Angular Gyrus	brain

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