Variant report

Variant	rs212058
Chromosome Location	chr3:60026959-60026960
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs172454	0.82[TSI][hapmap]
rs182418	0.88[CEU][hapmap]
rs212045	0.81[CHB][hapmap]
rs212049	0.94[CEU][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212054	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs212059	0.88[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs212064	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs212065	0.88[CEU][hapmap]
rs212066	0.88[CEU][hapmap]
rs3845972	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs6801817	0.83[CHB][hapmap]
rs7433793	0.85[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[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	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	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
3	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
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS 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	1 gene(s)	inside rSNPs	diseases
5	nsv876839	chr3:60024084-60039488	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs212058	SYNPR	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60020200-60030000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:60021000-60031600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:60022200-60030000	Weak transcription	Thymus	Thymus
4	chr3:60023000-60028000	Weak transcription	Dnd41	blood
5	chr3:60026200-60027400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:60026200-60027600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr3:60026400-60027000	Enhancers	Fetal Thymus	thymus
8	chr3:60026600-60033600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:60026800-60027600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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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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