Variant report

Variant	rs6446086
Chromosome Location	chr3:59857932-59857933
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1385713	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17493	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs587775	1.00[ASN][1000 genomes]
rs615964	1.00[ASN][1000 genomes]
rs675411	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675774	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874238	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv460565	chr3:59842644-59877988	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv470616	chr3:59842644-59877988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv590385	chr3:59842644-59877988	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv590386	chr3:59846067-59912377	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 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	chr3:59850000-59864000	Weak transcription	Fetal Thymus	thymus
2	chr3:59852800-59859800	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr3:59854800-59867000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:59854800-59870800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:59855000-59865200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:59855600-59859400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:59856600-59859800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:59856800-59860200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:59857000-59858200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr3:59857200-59858200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:59857400-59858000	Strong transcription	Dnd41	blood
12	chr3:59857400-59859000	Genic enhancers	Primary T cells from cord blood	blood
13	chr3:59857800-59858000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:59857800-59858200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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