Variant report

Variant	rs9988866
Chromosome Location	chr11:18392983-18392984
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18389829..18393207-chr11:18415267..18417660,3	K562	blood:
2	chr11:18389913..18393253-chr11:18414767..18417568,3	K562	blood:

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10734259	0.90[EUR][1000 genomes]
rs10741741	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10741742	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10832917	0.85[EUR][1000 genomes]
rs10832921	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024634	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1140047	0.90[EUR][1000 genomes]
rs12286683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs12293544	0.94[EUR][1000 genomes]
rs1520884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs2061164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2124374	0.90[EUR][1000 genomes]
rs3740711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3802968	0.90[EUR][1000 genomes]
rs3825025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4150526	0.92[EUR][1000 genomes]
rs4150550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4150562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4150566	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150579	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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150588	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150609	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs4150612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4150650	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];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150653	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150673	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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4353250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4757637	1.00[CHB][hapmap]
rs4757645	0.86[CEU][hapmap]
rs6486419	0.89[EUR][1000 genomes]
rs7103375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7129995	0.90[EUR][1000 genomes]
rs7947378	0.94[EUR][1000 genomes]
rs9783347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv523373	chr11:18382911-18401531	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv1811183	chr11:18389643-18432437	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9988866	HPS5	cis	cerebellum	SCAN
rs9988866	GTF2H1	cis	cerebellum	SCAN
rs9988866	GTF2H1	cis	Esophagus Muscularis	GTEx
rs9988866	PIK3C2A	cis	cerebellum	SCAN
rs9988866	LDHA	cis	parietal	SCAN
rs9988866	NELL1	cis	parietal	SCAN
rs9988866	GTF2H1	cis	Esophagus Mucosa	GTEx
rs9988866	ABCC8	cis	parietal	SCAN
rs9988866	LDHAL6A	cis	cerebellum	SCAN
rs9988866	GTF2H1	cis	multi-tissue	Pritchard
rs9988866	GTF2H1	cis	parietal	SCAN
rs9988866	HPS5	cis	multi-tissue	Pritchard
rs9988866	GTF2H1	cis	lymphoblastoid	seeQTL
rs9988866	GTF2H1	cis	Stomach	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
3	chr11:18387600-18393200	Weak transcription	Gastric	stomach
4	chr11:18387600-18394000	Weak transcription	Fetal Stomach	stomach
5	chr11:18387600-18395400	Weak transcription	Lung	lung
6	chr11:18387600-18398600	Weak transcription	Ovary	ovary
7	chr11:18387600-18404200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:18387600-18404400	Weak transcription	Esophagus	oesophagus
9	chr11:18387600-18404800	Weak transcription	Pancreas	Pancrea
10	chr11:18387800-18404400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:18388000-18405000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:18388200-18393400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:18388200-18395000	Weak transcription	NHLF	lung
14	chr11:18388400-18402600	Weak transcription	Hela-S3	cervix
15	chr11:18388600-18394400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:18388800-18393000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:18388800-18404400	Weak transcription	Brain Anterior Caudate	brain
18	chr11:18389000-18393000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:18389000-18393400	Weak transcription	Brain Germinal Matrix	brain
20	chr11:18389200-18393000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr11:18389200-18394400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:18389200-18404600	Weak transcription	Thymus	Thymus
23	chr11:18389400-18394600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:18389400-18394800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:18389800-18393000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:18390000-18393000	Strong transcription	Primary T cells from cord blood	blood
27	chr11:18390000-18393000	Weak transcription	Brain Substantia Nigra	brain
28	chr11:18390000-18394200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:18390000-18404400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:18390000-18404400	Weak transcription	Fetal Brain Female	brain
31	chr11:18390200-18393000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:18390200-18393200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:18390200-18394200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:18390200-18404200	Weak transcription	Fetal Thymus	thymus
35	chr11:18390400-18393000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:18390400-18393400	Weak transcription	Dnd41	blood
37	chr11:18390400-18393600	Weak transcription	Placenta	Placenta
38	chr11:18390400-18394400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:18390400-18399800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:18390400-18400000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr11:18390400-18404000	Weak transcription	NHDF-Ad	bronchial
42	chr11:18390400-18404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:18390400-18404200	Weak transcription	HMEC	breast
44	chr11:18390400-18404600	Weak transcription	Primary B cells from cord blood	blood
45	chr11:18390400-18404800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:18390600-18404200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:18390600-18404200	Weak transcription	Adipose Nuclei	Adipose
48	chr11:18390600-18404200	Weak transcription	Osteobl	bone
49	chr11:18390800-18404200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:18391200-18395200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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