Variant report

Variant	rs2018972
Chromosome Location	chr11:17535757-17535758
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1076311	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766408	0.84[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs11024315	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072234	0.84[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2190453	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104083	1.00[ASW][hapmap];0.88[CEU][hapmap];0.98[GIH][hapmap];0.87[LWK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs733874	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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
rs2018972	USH1C	cis	Thyroid	GTEx
rs2018972	NAV2	cis	parietal	SCAN

Chromatin state (count:24 , 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	chr11:17526600-17536600	Weak transcription	Brain Substantia Nigra	brain
4	chr11:17526600-17537200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:17527600-17549200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr11:17528800-17544000	Weak transcription	Gastric	stomach
7	chr11:17529800-17548600	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr11:17530600-17536600	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:17530800-17539800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:17531200-17536000	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr11:17531600-17547200	Strong transcription	Fetal Intestine Large	intestine
12	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:17532200-17547200	Strong transcription	Fetal Intestine Small	intestine
14	chr11:17533400-17539400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:17533600-17537400	Weak transcription	Spleen	Spleen
16	chr11:17533600-17537600	Weak transcription	Colonic Mucosa	Colon
17	chr11:17533600-17541800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:17533800-17539400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:17534400-17536200	Weak transcription	Brain Angular Gyrus	brain
20	chr11:17535000-17538400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr11:17535200-17537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:17535400-17542400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr11:17535600-17536600	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:17535600-17540600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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