Variant report

Variant	rs239542
Chromosome Location	chr6:80674848-80674849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12529133	1.00[YRI][hapmap]
rs151584	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs151673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17254634	1.00[YRI][hapmap]
rs186915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2082700	0.85[CEU][hapmap]
rs239507	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs239509	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239540	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240308	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240323	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs647044	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7765797	1.00[YRI][hapmap]

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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv3475140	chr6:80592690-80679283	Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3475142	chr6:80592789-80679132	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv965652	chr6:80663704-80688769	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region lncRNA	2 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	chr6:80672400-80676200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:80673200-80677000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:80673800-80676000	Flanking Active TSS	Dnd41	blood
4	chr6:80674200-80675000	Enhancers	Primary T cells from cord blood	blood
5	chr6:80674200-80675000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:80674200-80675200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:80674400-80675200	Active TSS	Thymus	Thymus
8	chr6:80674800-80675400	Flanking Active TSS	Fetal Thymus	thymus
9	chr6:80674800-80675600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:80674800-80676200	Enhancers	Primary T helper memory cells from peripheral blood 1	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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