Variant report

Variant	rs289698
Chromosome Location	chr1:76599096-76599097
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1631357	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs167050	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs172334	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs188333	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs289682	1.00[JPT][hapmap]
rs289683	1.00[JPT][hapmap]
rs289690	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs289699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs289701	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs291066	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2992502	1.00[JPT][hapmap]
rs2992503	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3011994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3011995	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs387214	1.00[JPT][hapmap]
rs389899	1.00[JPT][hapmap]
rs399529	0.91[ASN][1000 genomes]
rs418644	1.00[JPT][hapmap]
rs423152	1.00[JPT][hapmap]
rs447383	1.00[CHD][hapmap]
rs502421	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs597362	1.00[JPT][hapmap]
rs613909	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs622212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681280	1.00[JPT][hapmap]
rs817822	0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs860154	1.00[JPT][hapmap]
rs915402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs915403	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs915404	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1488	chr1:76587622-76632635	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv947432	chr1:76591253-76601907	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Mitochondrial DNA levels	25240745	GWAS catalog

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:76575400-76606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:76576600-76620000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76587800-76602800	Weak transcription	Right Atrium	heart
5	chr1:76588200-76615600	Weak transcription	Left Ventricle	heart
6	chr1:76591200-76607800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:76591800-76601400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:76592000-76601400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:76592600-76610800	Weak transcription	Fetal Kidney	kidney
10	chr1:76592800-76605800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:76593000-76601200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:76593000-76608200	Weak transcription	Fetal Lung	lung
13	chr1:76594000-76601200	Weak transcription	Brain Angular Gyrus	brain
14	chr1:76594000-76601600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:76594200-76601400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:76594200-76601400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:76594200-76607400	Weak transcription	Fetal Brain Female	brain
18	chr1:76594600-76615400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:76595600-76602400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:76596800-76601200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:76597000-76599800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:76598600-76609800	Weak transcription	Fetal Stomach	stomach

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