Variant report

Variant	rs10489556
Chromosome Location	chr1:70177006-70177007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12023616	0.87[GIH][hapmap]
rs12044761	0.84[GIH][hapmap]
rs12749989	0.86[EUR][1000 genomes]
rs1884581	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33980914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34174107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34227213	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34324965	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34491711	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34768080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35445128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35710092	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71651423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71651424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71651426	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515290	0.87[GIH][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	nsv949691	chr1:69749722-70302201	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3384194	chr1:69885024-70275430	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010921	chr1:70148694-70182578	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv998121	chr1:70154234-70182578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70173200-70194000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:70174400-70178800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:70176000-70177600	Enhancers	Psoas Muscle	Psoas
4	chr1:70176000-70177800	Enhancers	Fetal Intestine Small	intestine
5	chr1:70176000-70178400	Enhancers	Left Ventricle	heart
6	chr1:70176000-70178600	Enhancers	Fetal Heart	heart
7	chr1:70176200-70177200	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:70176200-70177600	Enhancers	Fetal Stomach	stomach
9	chr1:70176400-70177200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:70176400-70177600	Enhancers	Brain Angular Gyrus	brain
11	chr1:70176400-70178000	Enhancers	Ovary	ovary
12	chr1:70176600-70177600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:70176600-70177600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:70176800-70177200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:70176800-70177200	Enhancers	Fetal Kidney	kidney
16	chr1:70176800-70177400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:70176800-70177800	Enhancers	Fetal Lung	lung
18	chr1:70177000-70177200	Enhancers	Brain Anterior Caudate	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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