Variant report

Variant	rs3809401
Chromosome Location	chr14:70511406-70511407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10129447	0.84[ASN][1000 genomes]
rs10142899	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[ASN][1000 genomes]
rs1122271	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11629291	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs12435978	0.83[CHD][hapmap]
rs12883884	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[ASN][1000 genomes]
rs227434	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs2839867	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs7141091	0.80[CHD][hapmap]
rs7142759	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs8010945	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs8014694	0.83[CHD][hapmap]
rs8020841	0.90[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs998919	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[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	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3809401	ADAM21	cis	parietal	SCAN
rs3809401	SMOC1	cis	cerebellum	SCAN
rs3809401	RGS6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70500400-70512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:70509200-70514200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr14:70510200-70511600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:70510200-70512600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:70510800-70511800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr14:70510800-70515400	Weak transcription	Fetal Brain Female	brain
7	chr14:70511200-70513800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:70511200-70518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr14:70511400-70512800	Strong transcription	Psoas Muscle	Psoas

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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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