Variant report

Variant	rs6794085
Chromosome Location	chr3:53649608-53649609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11918955	0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.93[ASN][1000 genomes]
rs11919569	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12486029	0.93[ASN][1000 genomes]
rs1460115	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17053263	0.93[ASN][1000 genomes]
rs35836778	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3774468	0.85[CHB][hapmap]
rs3774473	0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs3774474	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3796345	0.90[MEX][hapmap]
rs58339775	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251907	0.84[ASN][1000 genomes]
rs62251908	0.93[ASN][1000 genomes]
rs7610071	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6794085	SELK	cis	parietal	SCAN
rs6794085	UBA7	cis	cerebellum	SCAN
rs6794085	TWF2	cis	parietal	SCAN
rs6794085	AMIGO3	cis	parietal	SCAN
rs6794085	DUSP23	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53635400-53650200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:53639400-53650200	Weak transcription	Fetal Intestine Small	intestine
3	chr3:53640000-53650800	Weak transcription	Fetal Intestine Large	intestine
4	chr3:53641200-53650000	Weak transcription	Fetal Lung	lung
5	chr3:53645400-53651000	Weak transcription	Lung	lung
6	chr3:53646800-53651000	Weak transcription	Spleen	Spleen
7	chr3:53647000-53650200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:53647000-53650400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:53648800-53650000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:53648800-53651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:53649000-53650000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:53649400-53650200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:53649600-53649800	Enhancers	Colonic Mucosa	Colon
14	chr3:53649600-53650000	Enhancers	Brain Hippocampus Middle	brain
15	chr3:53649600-53651200	Enhancers	Primary monocytes fromperipheralblood	blood

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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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