Variant report

Variant	rs62135398
Chromosome Location	chr2:48950075-48950076
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11680604	0.91[ASN][1000 genomes]
rs17398267	0.91[ASN][1000 genomes]
rs4374421	0.96[ASN][1000 genomes]
rs4490239	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4637173	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55983902	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62135381	0.91[ASN][1000 genomes]
rs62135383	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62135388	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62135389	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62135390	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135392	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62135397	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62135399	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714440	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6714821	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742911	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6761185	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557060	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559583	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567975	0.96[ASN][1000 genomes]
rs7567983	0.96[ASN][1000 genomes]
rs7571983	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578785	0.96[ASN][1000 genomes]
rs7584253	0.91[ASN][1000 genomes]
rs7595747	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608186	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv817851	chr2:48941428-48973127	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48943200-48953000	Weak transcription	K562	blood
2	chr2:48943400-48955400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:48943400-48956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:48945400-48955600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:48946200-48950400	Weak transcription	Fetal Lung	lung
6	chr2:48947000-48955400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:48947200-48951600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:48947200-48956000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:48947400-48955800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:48947600-48956000	Weak transcription	Brain Anterior Caudate	brain
11	chr2:48947600-48956600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:48947800-48955400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:48948000-48951800	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:48948400-48951200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:48949200-48951600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:48949400-48950200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr2:48949400-48951000	Enhancers	Stomach Smooth Muscle	stomach
18	chr2:48949400-48951000	Enhancers	Osteobl	bone
19	chr2:48949400-48951200	Enhancers	NHDF-Ad	bronchial
20	chr2:48949600-48950400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:48949600-48950400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:48949600-48950600	Enhancers	Ovary	ovary
23	chr2:48949600-48950600	Enhancers	NH-A	brain
24	chr2:48949600-48950800	Enhancers	Adipose Nuclei	Adipose
25	chr2:48949600-48951000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:48949800-48950200	Enhancers	Placenta	Placenta
27	chr2:48949800-48950600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:48949800-48951000	Enhancers	NHLF	lung
29	chr2:48949800-48955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:48950000-48950200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:48950000-48950600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:48950000-48950600	Enhancers	Fetal Kidney	kidney
33	chr2:48950000-48950800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:48950000-48955800	Weak transcription	Fetal Stomach	stomach

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