Variant report

Variant	rs6518796
Chromosome Location	chr22:33181302-33181303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000100150	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000100234	Chromatin interaction
ENSG00000100225	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2413156	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749509	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754282	0.82[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5754283	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518797	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9619311	0.82[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061384	chr22:33165464-33191811	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6518796	GAL3ST1	cis	parietal	SCAN
rs6518796	SEC14L4	cis	parietal	SCAN
rs6518796	SLC5A1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33174200-33184600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr22:33176400-33181600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr22:33176600-33181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:33176600-33184800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:33176800-33181800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:33176800-33182800	Enhancers	HepG2	liver
7	chr22:33176800-33185200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:33176800-33191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr22:33176800-33196600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr22:33177400-33192800	Weak transcription	Pancreas	Pancrea
11	chr22:33177600-33184600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr22:33178000-33181400	Weak transcription	Adipose Nuclei	Adipose
13	chr22:33179800-33186200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr22:33180000-33181800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr22:33180600-33181400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr22:33180600-33184800	Weak transcription	Lung	lung
17	chr22:33180800-33182000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr22:33180800-33182200	Enhancers	Placenta	Placenta
19	chr22:33180800-33182400	Enhancers	Fetal Stomach	stomach

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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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