Variant report

Variant	rs3753519
Chromosome Location	chr1:209875515-209875516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10082169	0.82[ASN][1000 genomes]
rs10082248	0.81[CHB][hapmap]
rs10863782	0.81[GIH][hapmap]
rs2235543	0.95[CHB][hapmap]
rs4844880	0.84[GIH][hapmap]
rs760951	0.95[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3753519	YOD1	cis	parietal	SCAN
rs3753519	TRAF3IP3	cis	cerebellum	SCAN
rs3753519	RASSF5	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209870800-209880000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209870800-209880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:209871000-209877400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:209874000-209877200	Weak transcription	Ovary	ovary
5	chr1:209874200-209877200	Weak transcription	Adipose Nuclei	Adipose
6	chr1:209875200-209875800	Enhancers	Thymus	Thymus
7	chr1:209875200-209876000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:209875200-209877200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:209875200-209877800	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:209875200-209878000	Enhancers	Brain Hippocampus Middle	brain
11	chr1:209875200-209882400	Enhancers	Brain Substantia Nigra	brain
12	chr1:209875400-209876000	Enhancers	Brain Anterior Caudate	brain
13	chr1:209875400-209877400	Weak transcription	Liver	Liver

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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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