Variant report

Variant	rs2240485
Chromosome Location	chr11:17538453-17538454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10766408	0.80[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs10832796	0.86[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2190454	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237965	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	0.88[CHB][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765642	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765643	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963401	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[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	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	esv33415	chr11:17532596-17549436	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2240485	USH1C	cis	lung	GTEx
rs2240485	MRGPRX2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
2	chr11:17526200-17539400	Weak transcription	Pancreas	Pancrea
3	chr11:17527600-17549200	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:17528800-17544000	Weak transcription	Gastric	stomach
5	chr11:17529800-17548600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr11:17530800-17539800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:17531600-17547200	Strong transcription	Fetal Intestine Large	intestine
8	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:17532200-17547200	Strong transcription	Fetal Intestine Small	intestine
10	chr11:17533400-17539400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:17533600-17541800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:17533800-17539400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:17535400-17542400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr11:17535600-17540600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:17536200-17542600	Enhancers	Brain Angular Gyrus	brain
16	chr11:17536400-17540200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr11:17536600-17539600	Enhancers	Brain Hippocampus Middle	brain
18	chr11:17536800-17542400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:17537200-17542000	Enhancers	Brain Cingulate Gyrus	brain
20	chr11:17537400-17538600	Enhancers	Spleen	Spleen
21	chr11:17537400-17544800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:17537400-17546800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:17538000-17542600	Enhancers	Brain Substantia Nigra	brain
24	chr11:17538200-17538600	Weak transcription	Brain Anterior Caudate	brain
25	chr11:17538200-17541200	Weak transcription	Colonic Mucosa	Colon
26	chr11:17538400-17538600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine

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