Variant report

Variant	rs6897671
Chromosome Location	chr5:59620281-59620282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10461451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1115372	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12054887	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12653863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13165296	0.81[GIH][hapmap]
rs13166747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13168480	0.99[ASN][1000 genomes]
rs13171028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13172481	0.81[GIH][hapmap]
rs1363862	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs1423246	0.93[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16874969	0.81[GIH][hapmap]
rs17839379	0.82[ASW][hapmap]
rs34353877	0.97[ASN][1000 genomes]
rs34762247	0.97[ASN][1000 genomes]
rs35811820	0.97[ASN][1000 genomes]
rs36050835	0.98[ASN][1000 genomes]
rs4349679	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4394088	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4409049	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs4580739	0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57237852	0.97[ASN][1000 genomes]
rs6449466	0.97[ASN][1000 genomes]
rs6449467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6449468	0.97[ASN][1000 genomes]
rs6860887	0.83[EUR][1000 genomes]
rs6862735	0.81[GIH][hapmap]
rs6878055	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7711093	0.81[GIH][hapmap]
rs7714394	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7733705	0.81[GIH][hapmap]
rs7735149	0.97[ASN][1000 genomes]
rs7737905	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59619000-59623400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59619200-59620400	Enhancers	Aorta	Aorta
3	chr5:59619200-59621200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:59619600-59621200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:59620000-59623600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:59620000-59625000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:59620200-59620400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:59620200-59620600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:59620200-59620600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:59620200-59620600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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