Variant report

Variant	rs10766393
Chromosome Location	chr11:17404652-17404653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:17401527..17405179-chr11:17405771..17408702,5	K562	blood:
2	chr11:17403171..17405241-chr11:17406430..17408298,2	MCF-7	breast:
3	chr11:17399571..17401205-chr11:17403779..17406500,2	K562	blood:
4	chr11:17403459..17406167-chr11:17526057..17528257,2	K562	blood:
5	chr11:17404201..17406453-chr11:17548482..17550709,2	K562	blood:
6	chr11:17404429..17405006-chr11:17525398..17526266,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP1-239B22.1.1-1	chr11:17402196-17405078	ENSG00000260196.1
2	lnc-RP1-239B22.1.1-1	chr11:17402953-17405078	NONHSAT018230

No data

Variant related genes	Relation type
ENSG00000187486	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1002227	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466382	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[MKK][hapmap]
rs10734253	0.93[ASN][1000 genomes]
rs10766383	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap]
rs10766384	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap]
rs10766385	0.82[ASW][hapmap];0.90[CEU][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap]
rs10766389	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs10766391	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10766392	0.90[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766395	0.95[ASN][1000 genomes]
rs10766396	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832757	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap]
rs10832765	0.82[ASW][hapmap];0.89[CEU][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap]
rs10832768	0.82[ASW][hapmap];0.90[CEU][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap]
rs10832769	0.89[CEU][hapmap]
rs10832770	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs10832779	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10832784	0.97[ASN][1000 genomes]
rs10832785	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11024251	0.90[CEU][hapmap]
rs11024273	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024275	0.80[EUR][1000 genomes]
rs1557764	0.97[ASN][1000 genomes]
rs2067043	0.81[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2074312	0.81[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs2074313	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2079042	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2214295	0.95[ASN][1000 genomes]
rs2285676	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34327804	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35762444	0.91[ASN][1000 genomes]
rs3741203	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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282912	0.85[EUR][1000 genomes]
rs4148638	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs5210	0.93[ASN][1000 genomes]
rs5218	1.00[ASW][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5222	0.91[ASN][1000 genomes]
rs7112030	0.87[ASN][1000 genomes]
rs7112138	0.87[ASN][1000 genomes]
rs71484767	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs886288	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9633836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645621	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10766393	KCNJ11	cis	Esophagus Mucosa	GTEx
rs10766393	ABCC8	cis	parietal	SCAN
rs10766393	LOC494141	cis	lymphoblastoid	seeQTL
rs10766393	PTH	cis	cerebellum	SCAN
rs10766393	RP1-239B22.5	cis	Esophagus Mucosa	GTEx
rs10766393	NUCB2	cis	cerebellum	SCAN
rs10766393	DKFZp686O24166	cis	cerebellum	SCAN
rs10766393	GTF2H1	cis	cerebellum	SCAN
rs10766393	ABCC8	cis	cerebellum	SCAN
rs10766393	TSG101	cis	cerebellum	SCAN
rs10766393	GTF2H1	cis	parietal	SCAN
rs10766393	KCNJ11	cis	cerebellum	SCAN
rs10766393	NCR3LG1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17394200-17407600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:17394400-17405000	Weak transcription	Brain Angular Gyrus	brain
3	chr11:17394400-17410200	Weak transcription	A549	lung
4	chr11:17395200-17405200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:17395200-17405800	Weak transcription	Gastric	stomach
6	chr11:17395200-17410200	Weak transcription	Thymus	Thymus
7	chr11:17395600-17406200	Weak transcription	Pancreas	Pancrea
8	chr11:17395600-17410200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:17395600-17410400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:17395800-17405200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr11:17395800-17405400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:17395800-17405400	Weak transcription	Left Ventricle	heart
13	chr11:17395800-17409200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:17396000-17408800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:17396600-17410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:17397200-17404800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:17397200-17407800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:17398200-17410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:17398400-17405400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr11:17398800-17410200	Weak transcription	Primary T cells from cord blood	blood
21	chr11:17400600-17408000	Strong transcription	Fetal Intestine Small	intestine
22	chr11:17400600-17408800	Weak transcription	Brain Germinal Matrix	brain
23	chr11:17400800-17407200	Weak transcription	Fetal Brain Female	brain
24	chr11:17400800-17410200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:17401000-17405600	Weak transcription	Brain Hippocampus Middle	brain
26	chr11:17401000-17410200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:17401200-17405200	Weak transcription	Brain Anterior Caudate	brain
28	chr11:17401200-17405400	Weak transcription	Psoas Muscle	Psoas
29	chr11:17401200-17407200	Weak transcription	Lung	lung
30	chr11:17401600-17405200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:17401600-17405200	Strong transcription	Dnd41	blood
32	chr11:17401600-17410200	Weak transcription	Hela-S3	cervix
33	chr11:17401600-17410200	Weak transcription	K562	blood
34	chr11:17401800-17405200	Weak transcription	NHEK	skin
35	chr11:17401800-17405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:17401800-17405600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:17401800-17407400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:17401800-17407400	Weak transcription	HepG2	liver
39	chr11:17401800-17410200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:17402000-17404800	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:17402000-17410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:17402000-17410200	Weak transcription	HMEC	breast
43	chr11:17402400-17407800	Weak transcription	Fetal Intestine Large	intestine
44	chr11:17403000-17405000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:17403000-17405400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:17403000-17410400	Weak transcription	Aorta	Aorta
47	chr11:17403200-17405200	Weak transcription	Fetal Brain Male	brain
48	chr11:17403200-17406200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr11:17403600-17408600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr11:17403800-17405200	Weak transcription	Esophagus	oesophagus

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