Variant report

Variant	rs12493744
Chromosome Location	chr3:53660030-53660031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11130374	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130375	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12486029	0.84[EUR][1000 genomes]
rs12486415	0.82[CHB][hapmap]
rs12492502	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs12496519	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2077167	0.96[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2680658	0.82[CHB][hapmap]
rs2680672	0.82[CHB][hapmap]
rs3774479	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs3796345	0.92[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs3821854	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6762231	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775765	0.82[EUR][1000 genomes]
rs6793312	0.82[CHB][hapmap]
rs6806330	0.82[CHB][hapmap]
rs735652	0.80[CHB][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	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
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12493744	MTNR1B	trans	cerebellum	SCAN
rs12493744	IL17RD	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53652800-53684000	Weak transcription	Right Atrium	heart
2	chr3:53653200-53660400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:53657800-53661400	Strong transcription	Fetal Intestine Large	intestine
4	chr3:53658600-53660200	Enhancers	Brain Germinal Matrix	brain
5	chr3:53659000-53660400	Weak transcription	Fetal Lung	lung
6	chr3:53659000-53662400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:53659000-53662800	Weak transcription	Fetal Brain Male	brain
8	chr3:53659200-53663400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:53659400-53664600	Weak transcription	Fetal Kidney	kidney
10	chr3:53659600-53662800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:53659600-53662800	Weak transcription	Fetal Brain Female	brain
12	chr3:53659600-53663400	Weak transcription	Lung	lung
13	chr3:53659600-53663600	Weak transcription	Pancreas	Pancrea
14	chr3:53659800-53661600	Enhancers	Stomach Mucosa	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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