Variant report

Variant	rs6860907
Chromosome Location	chr5:59069783-59069784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10043265	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs10043283	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs1027747	0.96[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10514857	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11949859	0.84[ASN][1000 genomes]
rs12187752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12188131	0.88[ASN][1000 genomes]
rs13155799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13168347	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1362941	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs1362942	0.88[ASN][1000 genomes]
rs1437124	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1504982	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504984	0.90[ASN][1000 genomes]
rs16877195	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[ASN][1000 genomes]
rs17369708	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs17381667	0.83[CHB][hapmap]
rs17381695	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs17381723	0.81[ASN][1000 genomes]
rs17382202	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs17440909	0.83[CHB][hapmap]
rs17441217	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs17441825	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs17742120	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs17742544	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs17743216	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs17799161	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs2164660	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs28583502	0.93[ASN][1000 genomes]
rs2938780	0.96[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2938783	0.86[GIH][hapmap]
rs2963825	0.80[EUR][1000 genomes]
rs2963826	0.96[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs298063	0.82[TSI][hapmap]
rs298084	0.82[TSI][hapmap]
rs298091	0.84[TSI][hapmap]
rs36143327	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3898713	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[ASN][1000 genomes]
rs4577665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699943	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs4700340	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs4700341	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs4700342	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55704150	0.93[ASN][1000 genomes]
rs55868825	0.88[ASN][1000 genomes]
rs56199003	0.88[ASN][1000 genomes]
rs6450528	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6450530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874708	0.96[ASN][1000 genomes]
rs6889294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6897073	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs72751211	0.84[ASN][1000 genomes]
rs72751218	0.84[ASN][1000 genomes]
rs72751226	0.85[ASN][1000 genomes]
rs72751229	0.88[ASN][1000 genomes]
rs72751231	0.88[ASN][1000 genomes]
rs72751232	0.88[ASN][1000 genomes]
rs72751233	0.88[ASN][1000 genomes]
rs72751234	0.88[ASN][1000 genomes]
rs72751235	0.88[ASN][1000 genomes]
rs72751237	0.88[ASN][1000 genomes]
rs72751241	0.88[ASN][1000 genomes]
rs72751244	0.88[ASN][1000 genomes]
rs72751247	0.88[ASN][1000 genomes]
rs72751250	0.88[ASN][1000 genomes]
rs72751252	0.91[ASN][1000 genomes]
rs72751264	0.88[ASN][1000 genomes]
rs756211	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs756212	0.83[CHB][hapmap];0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs7708952	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710199	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7736817	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs877745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981230	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.96[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	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59065200-59072800	Weak transcription	Aorta	Aorta
2	chr5:59065800-59070000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:59066000-59070400	Enhancers	Hela-S3	cervix
4	chr5:59066000-59081200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:59067400-59070000	Enhancers	NHEK	skin
6	chr5:59067600-59070000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr5:59068200-59085800	Weak transcription	Primary B cells from cord blood	blood
8	chr5:59069200-59070000	Enhancers	A549	lung
9	chr5:59069200-59071600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:59069200-59072400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:59069200-59073000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:59069200-59081400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:59069400-59069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:59069400-59072600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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