Variant report

Variant	rs9880557
Chromosome Location	chr3:59892271-59892272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13313997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13319697	0.87[AFR][1000 genomes]
rs9855887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869351	1.00[AFR][1000 genomes]
rs9876202	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1002104	chr3:59875996-59907597	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	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	chr3:59873200-59904200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:59883200-59893000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:59886800-59892600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:59889600-59893200	ZNF genes & repeats	Dnd41	blood
5	chr3:59890600-59903600	Weak transcription	Fetal Thymus	thymus
6	chr3:59891000-59892800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:59891200-59897600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:59891800-59892600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:59891800-59893200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:59891800-59893400	Enhancers	Fetal Brain Male	brain

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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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