Variant report

Variant	rs2072230
Chromosome Location	chr11:17518525-17518526
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10741728	0.87[EUR][1000 genomes]
rs1076204	0.88[EUR][1000 genomes]
rs10766404	0.87[EUR][1000 genomes]
rs10766405	0.87[EUR][1000 genomes]
rs10766406	0.92[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs10832795	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11603988	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1859091	0.88[EUR][1000 genomes]
rs2072227	0.84[CEU][hapmap]
rs2072228	0.81[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2188966	0.93[GIH][hapmap]
rs3758949	0.95[GIH][hapmap]
rs4756895	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4757521	0.85[EUR][1000 genomes]
rs4757523	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4757524	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv467714	chr11:17513147-17521825	Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv553585	chr11:17513147-17521825	Bivalent Enhancer Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2072230	SAAL1	cis	cerebellum	SCAN
rs2072230	ABCC8	cis	parietal	SCAN
rs2072230	TPH1	cis	parietal	SCAN
rs2072230	SAA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17511200-17526000	Weak transcription	Brain Substantia Nigra	brain
2	chr11:17512600-17530000	Weak transcription	Right Atrium	heart
3	chr11:17513600-17530600	Strong transcription	Fetal Intestine Small	intestine
4	chr11:17514800-17522800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:17515000-17523600	Weak transcription	Dnd41	blood
6	chr11:17515600-17524600	Strong transcription	Fetal Intestine Large	intestine
7	chr11:17515800-17518600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr11:17516000-17519600	Weak transcription	Gastric	stomach
9	chr11:17516000-17523000	Strong transcription	Duodenum Mucosa	Duodenum
10	chr11:17516800-17529600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
12	chr11:17517200-17519000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:17517800-17519000	Strong transcription	Colonic Mucosa	Colon
14	chr11:17518000-17522800	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr11:17518400-17519600	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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