Variant report

Variant	rs2406557
Chromosome Location	chr5:80614356-80614357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10041138	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10052929	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10061143	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10062967	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10072332	0.88[ASN][1000 genomes]
rs1039326	0.92[JPT][hapmap]
rs12514420	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516414	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs12519433	0.83[CEU][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1566433	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16876403	0.89[CHB][hapmap]
rs17228569	0.82[CEU][hapmap]
rs2124888	0.85[CEU][hapmap]
rs2270824	0.90[CHB][hapmap]
rs2277037	0.89[CHB][hapmap]
rs2291942	0.80[CHB][hapmap]
rs3756636	0.81[CEU][hapmap]
rs4502795	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703828	0.90[CHB][hapmap]
rs4704711	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4704713	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4704714	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4704717	0.89[CHB][hapmap]
rs56938600	0.89[ASN][1000 genomes]
rs57266451	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6863732	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868743	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868762	0.84[CEU][hapmap]
rs6871676	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877340	0.84[ASN][1000 genomes]
rs6889795	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896441	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896890	0.89[ASN][1000 genomes]
rs7718501	0.81[EUR][1000 genomes]
rs7731117	0.89[ASN][1000 genomes]
rs7734902	0.81[CEU][hapmap]
rs871701	0.84[JPT][hapmap]
rs955948	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 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	chr5:80608600-80615800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:80608600-80623000	Weak transcription	Psoas Muscle	Psoas
3	chr5:80610000-80614600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr5:80610000-80618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:80610600-80621800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:80611200-80616000	Weak transcription	Liver	Liver
7	chr5:80611400-80614400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:80611600-80623600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:80611800-80619000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:80612200-80623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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