Variant report

Variant	rs9633836
Chromosome Location	chr11:17401087-17401088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:17401040-17401164	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:17400307-17401134	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:17400201-17401965	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:17399194-17402032	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17399571..17401205-chr11:17403779..17406500,2	K562	blood:
2	chr11:17392236..17395328-chr11:17396635..17401653,4	K562	blood:

Variant related genes	Relation type
ENSG00000260196	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1002227	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466382	0.90[CEU][hapmap]
rs10734253	0.93[ASN][1000 genomes]
rs10766383	0.90[CEU][hapmap]
rs10766384	0.90[CEU][hapmap]
rs10766385	0.90[CEU][hapmap]
rs10766389	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10766391	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10766392	0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766393	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]
rs10766395	0.95[ASN][1000 genomes]
rs10766396	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832757	0.90[CEU][hapmap]
rs10832765	0.89[CEU][hapmap]
rs10832768	0.90[CEU][hapmap]
rs10832769	0.90[CEU][hapmap]
rs10832770	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs10832779	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10832784	0.97[ASN][1000 genomes]
rs10832785	0.95[CHB][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[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024275	0.82[EUR][1000 genomes]
rs1557764	0.97[ASN][1000 genomes]
rs2067043	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2074312	0.81[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2074313	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2079042	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2214295	0.95[ASN][1000 genomes]
rs2285676	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34327804	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35762444	0.91[ASN][1000 genomes]
rs3741203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282912	0.86[EUR][1000 genomes]
rs4148638	0.84[CEU][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs5210	0.93[ASN][1000 genomes]
rs5218	0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5222	0.91[ASN][1000 genomes]
rs7112030	0.87[ASN][1000 genomes]
rs7112138	0.87[ASN][1000 genomes]
rs71484767	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs886288	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9645621	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9633836	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs9633836	KCNJ11	cis	Esophagus Mucosa	GTEx
rs9633836	RP1-239B22.5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17382400-17401200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:17394200-17401600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:17394200-17401800	Strong transcription	HepG2	liver
4	chr11:17394200-17407600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:17394400-17402600	Weak transcription	HUVEC	blood vessel
6	chr11:17394400-17403600	Weak transcription	NHLF	lung
7	chr11:17394400-17405000	Weak transcription	Brain Angular Gyrus	brain
8	chr11:17394400-17410200	Weak transcription	A549	lung
9	chr11:17394600-17401600	Strong transcription	K562	blood
10	chr11:17395000-17401200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:17395000-17402600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:17395200-17402400	Weak transcription	NHDF-Ad	bronchial
13	chr11:17395200-17402600	Weak transcription	Osteobl	bone
14	chr11:17395200-17405200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:17395200-17405800	Weak transcription	Gastric	stomach
16	chr11:17395200-17410200	Weak transcription	Thymus	Thymus
17	chr11:17395600-17406200	Weak transcription	Pancreas	Pancrea
18	chr11:17395600-17410200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:17395600-17410400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:17395800-17403600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr11:17395800-17405200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr11:17395800-17405400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:17395800-17405400	Weak transcription	Left Ventricle	heart
24	chr11:17395800-17409200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:17396000-17408800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:17396400-17402000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:17396600-17404600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr11:17396600-17410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:17397000-17401200	Strong transcription	Brain Anterior Caudate	brain
30	chr11:17397200-17404800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:17397200-17407800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr11:17397400-17402800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:17398200-17410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:17398400-17405400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:17398800-17410200	Weak transcription	Primary T cells from cord blood	blood
36	chr11:17399000-17401600	ZNF genes & repeats	Dnd41	blood
37	chr11:17399000-17404600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr11:17399200-17401200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:17399200-17404200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr11:17399600-17401200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:17399800-17401600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:17400000-17401200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:17400000-17401200	Enhancers	Psoas Muscle	Psoas
44	chr11:17400000-17401400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:17400000-17402000	Enhancers	Esophagus	oesophagus
46	chr11:17400200-17401600	Strong transcription	Hela-S3	cervix
47	chr11:17400200-17401600	Strong transcription	HSMM	muscle
48	chr11:17400200-17401800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr11:17400400-17402400	Strong transcription	Fetal Intestine Large	intestine
50	chr11:17400600-17401200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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