Variant report

Variant	rs6540887
Chromosome Location	chr1:215401853-215401854
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10127656	0.84[JPT][hapmap]
rs10779639	0.85[JPT][hapmap]
rs10779640	0.85[JPT][hapmap]
rs10779644	0.85[JPT][hapmap]
rs10779645	0.90[JPT][hapmap]
rs10779647	0.84[JPT][hapmap]
rs10864165	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10864166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864169	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11120499	0.84[JPT][hapmap]
rs11120508	0.84[JPT][hapmap]
rs11120511	0.84[JPT][hapmap]
rs11120513	0.84[JPT][hapmap]
rs11120519	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11120524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120530	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120533	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11120539	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11120541	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11120542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11120581	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs11583745	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11588455	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12026669	0.82[EUR][1000 genomes]
rs12026702	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12031308	0.82[JPT][hapmap]
rs12036046	0.93[ASN][1000 genomes]
rs12037855	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12038616	0.88[CEU][hapmap]
rs12038695	0.88[CEU][hapmap]
rs12044688	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12047082	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12049601	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12120091	0.85[JPT][hapmap]
rs12121761	0.90[JPT][hapmap]
rs12143339	0.85[JPT][hapmap]
rs12407482	0.80[EUR][1000 genomes]
rs12740245	0.92[CEU][hapmap]
rs12750276	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12752882	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753507	0.91[CEU][hapmap]
rs1339401	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1339405	0.85[JPT][hapmap]
rs1339406	0.89[JPT][hapmap]
rs1416653	0.84[EUR][1000 genomes]
rs1416654	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1416655	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1416661	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1538544	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1538547	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs17024500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2153244	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2363564	0.84[JPT][hapmap]
rs2363565	0.84[JPT][hapmap]
rs2885815	0.85[JPT][hapmap]
rs3933352	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4098470	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4098471	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4233309	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4411107	0.84[JPT][hapmap]
rs4446938	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4497183	0.83[JPT][hapmap]
rs4509553	0.85[JPT][hapmap]
rs4531266	0.84[JPT][hapmap]
rs4655391	0.85[JPT][hapmap]
rs4655392	0.85[JPT][hapmap]
rs4655397	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4655398	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4655399	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4655400	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5025775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6540886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6666828	0.85[JPT][hapmap]
rs6667764	0.85[JPT][hapmap]
rs6670661	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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672978	0.84[JPT][hapmap]
rs6674743	0.82[EUR][1000 genomes]
rs7417100	0.84[JPT][hapmap]
rs7513709	0.85[JPT][hapmap]
rs7522160	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7522552	0.88[CEU][hapmap]
rs7531046	0.84[EUR][1000 genomes]
rs7541543	0.84[JPT][hapmap]
rs7549136	0.85[JPT][hapmap]
rs946487	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs946488	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs946489	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs946490	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
2	nsv873170	chr1:215367248-215440975	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	nsv527715	chr1:215396543-215402022	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
4	nsv518732	chr1:215398012-215402022	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215380600-215408000	Weak transcription	Osteobl	bone
2	chr1:215388600-215408200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:215392000-215408000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:215394000-215407800	Weak transcription	NHDF-Ad	bronchial
5	chr1:215401400-215402000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr1:215401400-215402000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr1:215401800-215402000	Enhancers	H1 Cell Line	embryonic stem cell

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