Variant report

Variant	rs17258709
Chromosome Location	chr3:60052705-60052706
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13062539	0.89[EUR][1000 genomes]
rs13084717	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13100563	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17062101	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17062179	0.87[EUR][1000 genomes]
rs17258256	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17258872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34603508	0.89[EUR][1000 genomes]
rs35037895	0.88[EUR][1000 genomes]
rs35226385	0.81[EUR][1000 genomes]
rs35755790	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3856662	0.81[EUR][1000 genomes]
rs4345028	0.91[EUR][1000 genomes]
rs67030566	0.90[EUR][1000 genomes]
rs6779716	0.82[EUR][1000 genomes]
rs6779755	0.81[EUR][1000 genomes]
rs67984492	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093924	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73093941	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][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	esv13593	chr3:60050980-60057155	Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60045000-60054200	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr3:60048200-60054000	Enhancers	Dnd41	blood
3	chr3:60048800-60059400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:60049400-60053200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:60051600-60053200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:60051600-60062000	Weak transcription	Aorta	Aorta
7	chr3:60051800-60056200	Weak transcription	Thymus	Thymus
8	chr3:60051800-60058200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:60051800-60063000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:60052000-60058400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:60052000-60059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:60052200-60056600	Weak transcription	Fetal Thymus	thymus
13	chr3:60052200-60058000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:60052400-60052800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:60052400-60055000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:60052400-60055600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:60052400-60055800	Weak transcription	Primary T cells from cord 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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