Variant report

Variant	rs9609680
Chromosome Location	chr22:33408519-33408520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13054969	0.84[CHB][hapmap]
rs2016169	0.81[CHB][hapmap]
rs756550	0.82[CHB][hapmap]
rs916396	0.85[CHB][hapmap]
rs9607002	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9607007	0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9609651	0.80[CHB][hapmap]
rs9609652	0.81[CHB][hapmap]
rs9609653	0.81[CHB][hapmap]
rs9609654	0.82[CHB][hapmap]
rs9609656	0.85[CHB][hapmap]
rs9609678	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs9609679	0.86[JPT][hapmap];0.89[MEX][hapmap]
rs9609681	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9609689	0.84[GIH][hapmap]

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	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9609680	GATSL3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33402400-33414200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr22:33402600-33419400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr22:33402800-33409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:33402800-33414600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr22:33403000-33420000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr22:33403400-33408800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr22:33403400-33414000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:33403600-33415600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:33403800-33414600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:33403800-33417600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr22:33405400-33414600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr22:33406400-33414600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr22:33407400-33417000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr22:33408200-33411400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr22:33408400-33410200	Enhancers	HepG2	liver
16	chr22:33408400-33410800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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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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