Variant report

Variant	rs7025302
Chromosome Location	chr9:92903522-92903523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10820972	0.83[EUR][1000 genomes]
rs10992311	0.93[EUR][1000 genomes]
rs10992324	0.83[EUR][1000 genomes]
rs10992326	0.83[EUR][1000 genomes]
rs12341265	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331703	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571209	0.86[EUR][1000 genomes]
rs28680232	0.82[EUR][1000 genomes]
rs28820642	0.82[EUR][1000 genomes]
rs56822056	0.88[EUR][1000 genomes]
rs7037744	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851822	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7860895	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9785239	0.93[EUR][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	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv893563	chr9:92816727-92967125	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1051180	chr9:92869383-93141038	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv540169	chr9:92869383-93141038	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7025302	FGD3	cis	cerebellum	SCAN
rs7025302	SEMA4D	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92900400-92905200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:92902800-92904200	Enhancers	Colon Smooth Muscle	Colon
3	chr9:92903200-92904000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:92903400-92903600	Enhancers	iPS DF 6.9 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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