Variant report

Variant	rs11992999
Chromosome Location	chr8:122639443-122639444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10089014	0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10094125	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs10097083	0.85[ASN][1000 genomes]
rs11780881	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11781907	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784137	0.81[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs1871884	0.81[CEU][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2385924	0.81[CEU][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4255143	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437656	0.82[ASN][1000 genomes]
rs4474031	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618701	0.86[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4871210	0.81[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs62524931	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62524932	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62524935	0.85[ASN][1000 genomes]
rs62524936	0.85[ASN][1000 genomes]
rs6651224	0.81[CEU][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs6984484	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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6998348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7009945	0.80[ASN][1000 genomes]
rs7016481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016956	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7817920	0.82[ASN][1000 genomes]
rs7834455	0.81[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs7834907	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033501	chr8:122436332-122758651	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv831446	chr8:122535039-122711959	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11992999	KCNK17	trans	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:122615200-122644000	Weak transcription	Fetal Brain Male	brain
2	chr8:122616000-122640200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr8:122624800-122640800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr8:122626800-122643800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:122627400-122649800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr8:122629800-122641000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr8:122632000-122648800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:122636000-122642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:122636400-122639600	Weak transcription	Fetal Kidney	kidney
10	chr8:122636600-122640200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:122636600-122644000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr8:122636800-122640800	Weak transcription	NH-A	brain
13	chr8:122636800-122647600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:122637000-122640800	Weak transcription	A549	lung
15	chr8:122637000-122643000	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr8:122637200-122640000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr8:122637600-122642200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr8:122637800-122639800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:122637800-122640200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr8:122638000-122640800	Flanking Active TSS	NHDF-Ad	bronchial
21	chr8:122638000-122641800	Genic enhancers	Fetal Lung	lung
22	chr8:122638000-122643600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr8:122638200-122642000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:122638600-122640400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr8:122638600-122641200	Genic enhancers	HSMM	muscle
26	chr8:122638600-122641400	Enhancers	Brain Substantia Nigra	brain
27	chr8:122638800-122641000	Enhancers	Brain Hippocampus Middle	brain
28	chr8:122638800-122642600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr8:122639000-122640200	Genic enhancers	NHLF	lung
30	chr8:122639000-122640600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr8:122639000-122640600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:122639000-122640800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr8:122639000-122643800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr8:122639000-122644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr8:122639000-122644200	Genic enhancers	Osteobl	bone
36	chr8:122639200-122639800	Weak transcription	Fetal Muscle Leg	muscle
37	chr8:122639200-122640200	Weak transcription	HSMMtube	muscle
38	chr8:122639200-122643000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr8:122639200-122644200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr8:122639200-122651400	Weak transcription	Brain Anterior Caudate	brain
41	chr8:122639400-122640000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr8:122639400-122644000	Weak transcription	Fetal Stomach	stomach

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