Variant report

Variant	rs3903801
Chromosome Location	chr6:24559433-24559434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10456306	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11751325	0.84[ASW][hapmap]
rs12193738	0.90[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes]
rs12196913	0.84[ASW][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12199955	0.84[ASW][hapmap];0.80[MEX][hapmap]
rs34505453	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34829630	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62400513	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs807507	0.81[CEU][hapmap];0.81[JPT][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	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1020653	chr6:24557870-24638244	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3903801	C6orf62	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
2	chr6:24535200-24566600	Weak transcription	Brain Germinal Matrix	brain
3	chr6:24535200-24591200	Weak transcription	Fetal Brain Male	brain
4	chr6:24535600-24560600	Weak transcription	Brain Anterior Caudate	brain
5	chr6:24535600-24560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:24535600-24563200	Weak transcription	Brain Angular Gyrus	brain
7	chr6:24535600-24583400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:24539200-24583200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:24548400-24583400	Weak transcription	A549	lung
10	chr6:24550200-24566400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:24552600-24568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:24554600-24563600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:24559200-24559600	Enhancers	Pancreas	Pancrea
14	chr6:24559200-24559800	Strong transcription	Fetal Brain Female	brain

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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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