Variant report

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10766408	0.86[GIH][hapmap]
rs10832796	0.91[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2190454	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240485	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240486	0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3765642	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3765643	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs963401	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2237965	USH1C	cis	lung	GTEx
rs2237965	MRGPRX2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
2	chr11:17522600-17531800	Weak transcription	Colonic Mucosa	Colon
3	chr11:17525400-17533600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:17526200-17539400	Weak transcription	Pancreas	Pancrea
5	chr11:17526600-17536600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:17526600-17537200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:17527600-17549200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr11:17528800-17544000	Weak transcription	Gastric	stomach
9	chr11:17529800-17532400	Enhancers	Spleen	Spleen
10	chr11:17529800-17548600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr11:17530200-17533200	Weak transcription	Left Ventricle	heart
12	chr11:17530600-17531800	Weak transcription	HMEC	breast
13	chr11:17530600-17532200	Genic enhancers	Fetal Intestine Small	intestine
14	chr11:17530600-17533200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:17530600-17536600	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:17530800-17532800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:17530800-17533000	Weak transcription	Psoas Muscle	Psoas
18	chr11:17530800-17539800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:17531000-17531600	Weak transcription	Fetal Intestine Large	intestine
20	chr11:17531200-17536000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr11:17531400-17532200	Enhancers	Fetal Muscle Trunk	muscle

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