Variant report

Variant	rs12494652
Chromosome Location	chr3:116028380-116028381
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11924642	0.80[MEX][hapmap]
rs11928524	0.86[MEX][hapmap]
rs13070962	0.80[MEX][hapmap]
rs1367770	0.86[MEX][hapmap]
rs1731596	0.80[MEX][hapmap]
rs1993733	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2100807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4831092	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611085	1.00[CHB][hapmap]
rs7621652	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7634137	0.86[MEX][hapmap]
rs7637573	0.80[MEX][hapmap]
rs9809878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838534	0.80[MEX][hapmap]
rs9872860	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv3957	chr3:115986950-116032625	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12494652	C3orf30	cis	cerebellum	SCAN
rs12494652	NR1I2	cis	cerebellum	SCAN
rs12494652	KLHL11	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116017000-116029600	Enhancers	Colon Smooth Muscle	Colon
2	chr3:116019200-116028400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:116019600-116037000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:116022200-116033000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:116024000-116028600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:116025800-116028400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:116025800-116028400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:116026000-116031600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:116026000-116031600	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:116026200-116037200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:116026400-116034000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:116027000-116028800	Enhancers	Brain Substantia Nigra	brain
13	chr3:116027400-116028600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:116027400-116028800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:116028200-116037400	Weak transcription	Brain Germinal Matrix	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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