Variant report

Variant	rs357708
Chromosome Location	chr2:180664033-180664034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10153833	1.00[JPT][hapmap]
rs12053220	0.83[CHD][hapmap]
rs12466855	0.84[CHB][hapmap]
rs13014793	0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1352111	0.86[CHB][hapmap]
rs1486232	0.81[CEU][hapmap]
rs165380	0.81[CHD][hapmap]
rs1906012	0.89[JPT][hapmap]
rs357709	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs357712	0.86[CHB][hapmap]
rs357714	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6752731	0.88[JPT][hapmap]
rs7557122	0.88[JPT][hapmap]
rs7597666	0.88[JPT][hapmap]
rs7608363	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[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	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs357708	HOXD9	cis	parietal	SCAN
rs357708	NEUROD1	cis	cerebellum	SCAN
rs357708	PDE1A	cis	parietal	SCAN
rs357708	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180655600-180669600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:180661600-180665400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:180661600-180665400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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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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