Variant report

Variant	rs676959
Chromosome Location	chr2:234933559-234933560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10929331	0.91[ASN][1000 genomes]
rs11563200	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[ASN][1000 genomes]
rs11679031	0.83[ASN][1000 genomes]
rs17869074	0.81[YRI][hapmap]
rs28953469	0.81[YRI][hapmap]
rs582082	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs589763	0.90[ASN][1000 genomes]
rs591103	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs599294	0.91[ASN][1000 genomes]
rs602312	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs602371	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs663924	0.83[ASN][1000 genomes]
rs668355	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs676546	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs676896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677448	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679207	0.91[ASN][1000 genomes]
rs683719	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv834571	chr2:234929288-235110332	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460138	chr2:234933559-234944043	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv584709	chr2:234933559-234944043	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234931800-234933600	Weak transcription	Liver	Liver
2	chr2:234931800-234934000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr2:234931800-234938200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:234933000-234933600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:234933000-234934000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:234933000-234934200	Enhancers	Fetal Brain Male	brain
7	chr2:234933000-234934800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:234933000-234935600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:234933200-234933800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:234933200-234933800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:234933200-234934400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:234933400-234933600	Enhancers	NHEK	skin
13	chr2:234933400-234933800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:234933400-234933800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:234933400-234933800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr2:234933400-234934000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:234933400-234934000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:234933400-234934000	Enhancers	Primary T helper cells fromperipheralblood	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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