Variant report

Variant	rs333500
Chromosome Location	chr3:78864469-78864470
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12330466	1.00[AMR][1000 genomes]
rs12330828	1.00[AMR][1000 genomes]
rs13319888	1.00[AMR][1000 genomes]
rs162816	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs173004	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs231606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333473	1.00[AMR][1000 genomes]
rs333482	1.00[AMR][1000 genomes]
rs333492	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333494	1.00[AMR][1000 genomes]
rs333496	1.00[AMR][1000 genomes]
rs333504	1.00[AMR][1000 genomes]
rs333505	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs333509	1.00[AMR][1000 genomes]
rs365492	1.00[AMR][1000 genomes]
rs365924	1.00[AMR][1000 genomes]
rs375298	1.00[AMR][1000 genomes]
rs383189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs390060	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs408455	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs416640	1.00[AMR][1000 genomes]
rs72892483	1.00[AMR][1000 genomes]
rs72894478	0.83[AFR][1000 genomes]
rs72896415	1.00[AMR][1000 genomes]
rs9631524	1.00[AMR][1000 genomes]
rs9631525	1.00[AMR][1000 genomes]
rs9810277	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9813851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9817612	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9822237	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9849099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9863633	0.87[AFR][1000 genomes]
rs9872311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	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
3	nsv877019	chr3:78808850-78877217	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv432459	chr3:78819310-78874310	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78851400-78880400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:78854200-78865400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:78854200-78872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:78854400-78871200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:78855400-78872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:78860200-78871600	Weak transcription	HepG2	liver
7	chr3:78860800-78869600	Weak transcription	Fetal Brain Male	brain
8	chr3:78861000-78867600	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:78861000-78872600	Weak transcription	Brain Anterior Caudate	brain
10	chr3:78861600-78867400	Weak transcription	Fetal Stomach	stomach
11	chr3:78861800-78869800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:78862400-78869600	Weak transcription	Fetal Lung	lung
13	chr3:78863800-78865400	Enhancers	Brain Substantia Nigra	brain
14	chr3:78864000-78864800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr3:78864000-78865000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:78864000-78865400	Enhancers	Fetal Heart	heart
17	chr3:78864200-78864800	Enhancers	Brain Cingulate Gyrus	brain
18	chr3:78864200-78865000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:78864400-78865000	Enhancers	Brain Angular Gyrus	brain

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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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