Variant report

Variant	rs13421618
Chromosome Location	chr2:48945954-48945955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48899103..48900749-chr2:48945263..48947505,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11125180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13393141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13418626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13418782	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13421430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17326537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4303756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4339007	1.00[CHB][hapmap];0.80[JPT][hapmap];0.93[ASN][1000 genomes]
rs4352270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4531984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752933	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6760924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48921600-48949600	Weak transcription	Ovary	ovary
2	chr2:48941000-48946400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:48942800-48946400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48942800-48949200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:48943200-48949400	Weak transcription	Osteobl	bone
6	chr2:48943200-48950000	Weak transcription	Fetal Kidney	kidney
7	chr2:48943200-48953000	Weak transcription	K562	blood
8	chr2:48943400-48949800	Weak transcription	Fetal Stomach	stomach
9	chr2:48943400-48949800	Weak transcription	NHLF	lung
10	chr2:48943400-48955400	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:48943400-48956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:48943600-48946400	Weak transcription	NH-A	brain
13	chr2:48943600-48948600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:48944400-48946400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:48944400-48947800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:48945000-48946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:48945000-48946600	Weak transcription	Brain Substantia Nigra	brain
18	chr2:48945400-48946400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:48945400-48946400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:48945400-48946400	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:48945400-48947000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:48945400-48949600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:48945400-48955600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:48945600-48946000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:48945600-48946000	Weak transcription	Fetal Lung	lung
26	chr2:48945600-48946200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:48945600-48946800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:48945600-48946800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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