Variant report

Variant	rs289688
Chromosome Location	chr1:76585105-76585106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10493583	0.81[JPT][hapmap]
rs11162086	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs1251568	0.81[JPT][hapmap]
rs1251573	0.81[JPT][hapmap]
rs1335738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172358	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs289679	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs289689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289691	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291060	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3843263	0.84[CHB][hapmap]
rs384639	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413540	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs427589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441806	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55811644	0.81[ASN][1000 genomes]
rs901490	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518927	chr1:76573614-76586272	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv522056	chr1:76573614-76598209	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:76557600-76588800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:76575400-76606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:76576400-76587000	Weak transcription	Left Ventricle	heart
5	chr1:76576400-76591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:76576600-76620000	Weak transcription	Primary B cells from cord blood	blood
7	chr1:76577000-76590800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:76579400-76590800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:76579800-76590800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:76581000-76586800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:76581800-76596200	Weak transcription	Fetal Intestine Large	intestine
12	chr1:76583400-76590200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:76583600-76586400	Weak transcription	Fetal Lung	lung
14	chr1:76583600-76589800	Weak transcription	Brain Cingulate Gyrus	brain

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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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