Variant report

Variant	rs162423
Chromosome Location	chr3:78883774-78883775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1355983	0.81[CHB][hapmap]
rs1383406	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs1487135	0.88[CHB][hapmap];0.82[YRI][hapmap]
rs162262	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[YRI][hapmap]
rs162263	0.80[CHB][hapmap]
rs162268	0.80[CHB][hapmap]
rs162427	0.82[CEU][hapmap]
rs162428	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs162429	0.87[CHB][hapmap]
rs17311057	0.86[CHB][hapmap]
rs17311169	0.87[CHB][hapmap]
rs1825760	0.88[CHB][hapmap];0.82[YRI][hapmap]
rs2018432	0.88[CHB][hapmap];0.82[YRI][hapmap];0.80[ASN][1000 genomes]
rs2082973	0.88[CHB][hapmap];0.82[YRI][hapmap]
rs328045	0.80[CHB][hapmap]
rs328047	0.80[CHB][hapmap]
rs329805	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs329812	0.84[CEU][hapmap]
rs329813	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs329814	0.80[CHB][hapmap]
rs329819	0.87[CHB][hapmap]
rs329822	0.81[CHB][hapmap]
rs331134	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331158	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331199	0.80[CHB][hapmap]
rs333483	0.87[CHB][hapmap]
rs333493	0.87[CHB][hapmap]
rs333507	0.87[CHB][hapmap]
rs35556205	0.81[ASN][1000 genomes]
rs4681011	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681013	0.87[CEU][hapmap];0.93[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs498805	0.80[CHB][hapmap]
rs531125	0.85[YRI][hapmap]
rs6548600	0.85[CHB][hapmap]
rs6548601	0.81[CHB][hapmap]
rs6770452	0.87[CHB][hapmap];0.80[YRI][hapmap]
rs6772919	0.81[CHB][hapmap]
rs6805432	0.80[ASN][1000 genomes]
rs73117115	0.80[ASN][1000 genomes]
rs7610996	0.88[CHB][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7617433	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs7617538	0.80[CHB][hapmap]
rs7629522	0.87[CHB][hapmap];0.80[YRI][hapmap]
rs7638321	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7650002	0.87[CHB][hapmap]

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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78873200-78888800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:78875600-78884400	Weak transcription	NHDF-Ad	bronchial
3	chr3:78875600-78888800	Weak transcription	Fetal Lung	lung
4	chr3:78882000-78894800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:78882600-78885200	Enhancers	HepG2	liver
6	chr3:78882800-78883800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:78883200-78884400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:78883400-78888800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:78883600-78888800	Weak transcription	Brain Hippocampus Middle	brain

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