Variant report

Variant	rs12465172
Chromosome Location	chr2:53667972-53667973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11125496	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680345	0.80[AMR][1000 genomes]
rs11886009	0.80[ASN][1000 genomes]
rs11891803	0.80[ASN][1000 genomes]
rs12477071	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477543	0.90[EUR][1000 genomes]
rs12999083	0.80[ASN][1000 genomes]
rs13025722	0.80[ASN][1000 genomes]
rs13411752	0.82[ASN][1000 genomes]
rs1389572	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1402899	0.80[ASN][1000 genomes]
rs1521932	0.85[CEU][hapmap]
rs1521936	0.90[ASN][1000 genomes]
rs1521947	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1521949	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1521950	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4330141	0.80[ASN][1000 genomes]
rs4566397	0.80[ASN][1000 genomes]
rs4672418	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60013509	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6718796	0.80[AMR][1000 genomes]
rs6719172	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6748128	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6748135	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs909051	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv997401	chr2:53515629-53863347	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3383918	chr2:53585059-53710179	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv984438	chr2:53649278-53685651	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53662600-53669400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:53663000-53669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:53663600-53668800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:53663600-53669000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:53664200-53669000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:53664800-53669400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:53665600-53672800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:53665800-53668800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:53665800-53672800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:53666000-53671400	Weak transcription	Hela-S3	cervix
11	chr2:53667600-53668000	Enhancers	Brain Hippocampus Middle	brain
12	chr2:53667800-53675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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