Variant report

Variant	rs10766396
Chromosome Location	chr11:17413568-17413569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17413027..17414952-chr11:17415169..17417199,2	MCF-7	breast:
2	chr11:17377121..17379727-chr11:17413012..17415189,2	K562	blood:
3	chr11:17407226..17410020-chr11:17412106..17414514,2	K562	blood:

Variant related genes	Relation type
ENSG00000187486	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1002227	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10734253	0.82[ASN][1000 genomes]
rs10766391	0.81[EUR][1000 genomes]
rs10766392	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10766393	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10766395	0.84[ASN][1000 genomes]
rs10832779	0.81[EUR][1000 genomes]
rs10832784	0.82[ASN][1000 genomes]
rs10832785	0.82[ASN][1000 genomes]
rs11024273	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024275	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1557764	0.82[ASN][1000 genomes]
rs2067043	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2074312	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074313	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2079042	0.81[EUR][1000 genomes]
rs2214295	0.84[ASN][1000 genomes]
rs2285676	0.86[ASN][1000 genomes]
rs34327804	0.80[EUR][1000 genomes]
rs35762444	0.86[ASN][1000 genomes]
rs3741203	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41282912	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4148638	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5210	0.86[ASN][1000 genomes]
rs5218	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5222	0.84[ASN][1000 genomes]
rs7112030	0.87[ASN][1000 genomes]
rs7112138	0.87[ASN][1000 genomes]
rs886288	0.82[ASN][1000 genomes]
rs9633836	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv467712	chr11:17393644-17418477	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv553583	chr11:17393644-17418477	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv517772	chr11:17401134-17427862	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv897018	chr11:17403639-17417337	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv528959	chr11:17403639-17435214	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv540951	chr11:17404438-17422755	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv540952	chr11:17407913-17422755	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv467713	chr11:17408025-17440473	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv553584	chr11:17408025-17440473	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10766396	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs10766396	NCR3LG1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17410800-17417200	Weak transcription	Gastric	stomach
2	chr11:17411400-17416200	Weak transcription	Brain Anterior Caudate	brain
3	chr11:17411400-17422600	Weak transcription	Right Atrium	heart
4	chr11:17411600-17415400	Weak transcription	Brain Angular Gyrus	brain
5	chr11:17411800-17413800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:17411800-17414000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:17411800-17414400	Weak transcription	Spleen	Spleen
8	chr11:17411800-17414600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:17411800-17415200	Weak transcription	Fetal Brain Female	brain
10	chr11:17411800-17416200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:17411800-17417800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:17411800-17419000	Weak transcription	Brain Germinal Matrix	brain
13	chr11:17411800-17426000	Weak transcription	Lung	lung
14	chr11:17411800-17426000	Weak transcription	Pancreas	Pancrea
15	chr11:17411800-17426800	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:17411800-17426800	Weak transcription	Brain Substantia Nigra	brain
17	chr11:17411800-17435000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:17413000-17413600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:17413000-17413600	Enhancers	Primary B cells from peripheral blood	blood
20	chr11:17413200-17413600	Enhancers	GM12878-XiMat	blood
21	chr11:17413200-17432400	Weak transcription	Dnd41	blood

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