Variant report

Variant	rs6859677
Chromosome Location	chr5:5297967-5297968
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:17)

rs_ID	r²[population]
rs10068364	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10512780	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16875236	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35333017	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57251518	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60073863	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023579	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73039115	0.91[EUR][1000 genomes]
rs73039118	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73039119	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73039122	0.83[EUR][1000 genomes]
rs73039185	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73039191	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73041114	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73041130	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7737261	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1032719	chr5:5102763-5387406	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537621	chr5:5102763-5387406	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5272400-5298400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:5293000-5301800	Weak transcription	Ovary	ovary
3	chr5:5293200-5301800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:5293400-5302000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:5294800-5299600	Enhancers	Fetal Brain Male	brain
6	chr5:5296200-5299200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:5296600-5300000	Enhancers	HepG2	liver
8	chr5:5296800-5299600	Enhancers	Liver	Liver
9	chr5:5297000-5298000	Enhancers	Placenta Amnion	Placenta Amnion
10	chr5:5297000-5298400	Enhancers	Brain Angular Gyrus	brain
11	chr5:5297000-5298800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:5297200-5299600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:5297400-5298000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:5297400-5299600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:5297800-5298600	Enhancers	Brain Hippocampus Middle	brain
16	chr5:5297800-5299200	Enhancers	NH-A	brain
17	chr5:5297800-5299400	Enhancers	Fetal Lung	lung
18	chr5:5297800-5299400	Enhancers	Fetal Muscle Leg	muscle
19	chr5:5297800-5299800	Enhancers	Fetal Intestine Large	intestine

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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