Variant report

Variant	rs1055574
Chromosome Location	chr11:17515833-17515834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1055577	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1055581	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1064074	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10766406	0.82[CEU][hapmap]
rs11024309	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072225	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072227	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757525	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7943395	0.85[ASN][1000 genomes]
rs917277	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs985572	0.81[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1055574	TPH1	cis	parietal	SCAN
rs1055574	SAAL1	cis	cerebellum	SCAN
rs1055574	ABCC8	cis	parietal	SCAN

Chromatin state (count:11 , 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	chr11:17514200-17516000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr11:17514800-17522800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:17515000-17516200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr11:17515000-17523600	Weak transcription	Dnd41	blood
8	chr11:17515400-17517800	Weak transcription	Colonic Mucosa	Colon
9	chr11:17515600-17524600	Strong transcription	Fetal Intestine Large	intestine
10	chr11:17515800-17516000	Enhancers	Gastric	stomach
11	chr11:17515800-17518600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

Quick Search:

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

what's new

Quick links