Variant report

Variant	rs13406560
Chromosome Location	chr2:77241588-77241589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10520169	0.86[CHB][hapmap]
rs12713886	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713890	0.94[EUR][1000 genomes]
rs12713891	0.93[EUR][1000 genomes]
rs12987907	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12992834	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13013784	1.00[JPT][hapmap]
rs13021476	0.89[EUR][1000 genomes]
rs13033902	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13034088	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13388552	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13389562	0.86[ASN][1000 genomes]
rs13430336	0.80[JPT][hapmap]
rs1348828	0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1348829	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374390	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1374392	0.88[EUR][1000 genomes]
rs1374394	0.81[JPT][hapmap]
rs1446694	0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446700	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1446702	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1446704	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1446706	0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446713	0.85[EUR][1000 genomes]
rs1446714	0.85[EUR][1000 genomes]
rs1446717	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1446718	0.87[EUR][1000 genomes]
rs1446720	0.89[EUR][1000 genomes]
rs17013302	0.86[CHB][hapmap]
rs17013306	0.86[CHB][hapmap]
rs17013313	0.86[CHB][hapmap]
rs17013592	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17013595	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs17013599	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17013615	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17040496	0.89[EUR][1000 genomes]
rs17040500	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17089	0.82[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1838879	0.89[EUR][1000 genomes]
rs2044485	0.89[EUR][1000 genomes]
rs2197603	0.91[CHB][hapmap]
rs34287182	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34577944	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35458070	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4853290	0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58936967	0.89[EUR][1000 genomes]
rs6547106	0.85[EUR][1000 genomes]
rs6547107	0.89[EUR][1000 genomes]
rs6547108	0.86[EUR][1000 genomes]
rs6547109	0.89[EUR][1000 genomes]
rs6547111	0.89[EUR][1000 genomes]
rs6547113	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6547117	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs6547118	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs6706194	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724799	0.94[EUR][1000 genomes]
rs6737296	0.89[EUR][1000 genomes]
rs6739222	0.86[CHB][hapmap]
rs6741095	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6750979	0.85[EUR][1000 genomes]
rs6758707	0.89[EUR][1000 genomes]
rs72823154	0.89[EUR][1000 genomes]
rs7556871	0.85[EUR][1000 genomes]
rs7569919	0.94[EUR][1000 genomes]
rs7569994	0.92[EUR][1000 genomes]
rs7591186	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7595678	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7604936	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs985234	0.91[CHB][hapmap]

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	nsv834266	chr2:77120236-77287504	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv519950	chr2:77213103-77256291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv997284	chr2:77233426-77303198	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1007408	chr2:77235194-77255152	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77232000-77245600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:77237000-77243800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:77237000-77245400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:77237600-77243600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:77237800-77243600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:77238000-77245400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:77238200-77244000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:77238200-77244200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:77239200-77244200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:77240400-77243600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:77240600-77243400	Weak transcription	Fetal Lung	lung
12	chr2:77240600-77243600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:77240600-77244200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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