Variant report

Variant	rs16986172
Chromosome Location	chr22:28626219-28626220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10483144	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs10483149	0.91[YRI][hapmap]
rs134510	1.00[ASW][hapmap]
rs16985919	0.84[AFR][1000 genomes]
rs16985921	0.84[AFR][1000 genomes]
rs16986023	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16986030	0.87[AFR][1000 genomes]
rs16986041	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs16986116	0.80[AFR][1000 genomes]
rs16986128	0.93[AFR][1000 genomes]
rs16986168	1.00[AFR][1000 genomes]
rs16986181	1.00[AFR][1000 genomes]
rs16986193	0.93[AFR][1000 genomes]
rs16986219	0.93[AFR][1000 genomes]
rs16986231	0.93[AFR][1000 genomes]
rs16986238	1.00[AFR][1000 genomes]
rs16986240	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs16986246	0.93[AFR][1000 genomes]
rs16986249	0.93[AFR][1000 genomes]
rs16986259	0.93[AFR][1000 genomes]
rs16986349	0.93[AFR][1000 genomes]
rs16986405	1.00[MKK][hapmap];0.91[YRI][hapmap]
rs2092498	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2103601	0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs57301669	0.87[AFR][1000 genomes]
rs58713460	0.93[AFR][1000 genomes]
rs60811750	0.93[AFR][1000 genomes]
rs61317772	0.80[AFR][1000 genomes]
rs9625433	0.83[LWK][hapmap];0.91[YRI][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16986172	XBP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28612200-28634800	Weak transcription	Dnd41	blood
2	chr22:28615800-28626400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:28618400-28626800	Weak transcription	Fetal Kidney	kidney
4	chr22:28618400-28639600	Weak transcription	Ovary	ovary
5	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea
6	chr22:28619200-28626400	Weak transcription	Fetal Lung	lung
7	chr22:28619400-28631000	Weak transcription	Brain Hippocampus Middle	brain
8	chr22:28620400-28639200	Weak transcription	Left Ventricle	heart
9	chr22:28625400-28626600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr22:28625400-28628400	Enhancers	Adipose Nuclei	Adipose
11	chr22:28625400-28628600	Enhancers	HSMM	muscle
12	chr22:28625400-28628600	Enhancers	NHLF	lung
13	chr22:28625600-28626400	Enhancers	Aorta	Aorta
14	chr22:28625600-28626400	Enhancers	Fetal Muscle Leg	muscle
15	chr22:28625600-28626600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:28625600-28627000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr22:28625600-28627800	Enhancers	NH-A	brain
18	chr22:28625600-28628600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr22:28625600-28628800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:28625800-28630800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr22:28626000-28626400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr22:28626000-28626600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr22:28626000-28626600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr22:28626000-28626800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:28626000-28627000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr22:28626000-28627600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr22:28626000-28627600	Enhancers	Colon Smooth Muscle	Colon
28	chr22:28626200-28626400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:28626200-28626400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr22:28626200-28626400	Enhancers	Psoas Muscle	Psoas
31	chr22:28626200-28626400	Enhancers	HSMMtube	muscle
32	chr22:28626200-28626400	Enhancers	NHDF-Ad	bronchial
33	chr22:28626200-28626400	Enhancers	Osteobl	bone
34	chr22:28626200-28627000	Enhancers	Fetal Stomach	stomach
35	chr22:28626200-28628000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr22:28626200-28628600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:28626200-28628800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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