Variant report

Variant	rs6569775
Chromosome Location	chr6:132489527-132489528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:132269655-132282174..6:132486779-132489747	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000118523	Chromatin interaction
ENSG00000227220	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10214443	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12333213	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1321271	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1321273	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2064771	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2876172	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57273539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61584962	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6569776	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6916021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6920169	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6925799	1.00[EUR][1000 genomes]
rs6929585	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6937406	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6940428	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6940609	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6940746	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6941580	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551713	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7356898	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745229	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745523	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7751452	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7752512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7756259	0.83[EUR][1000 genomes]
rs7756584	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7756735	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7757338	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761015	1.00[EUR][1000 genomes]
rs7774777	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9321326	0.98[AFR][1000 genomes]
rs9321327	1.00[EUR][1000 genomes]
rs9483389	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483391	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483394	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483395	0.83[AMR][1000 genomes]
rs9483397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483404	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9483409	0.83[AMR][1000 genomes]
rs9493189	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493191	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493192	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493193	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493194	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493195	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493197	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493201	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493202	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493205	1.00[EUR][1000 genomes]
rs9493207	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493210	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493214	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9493215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493217	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9493219	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493220	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493221	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493222	1.00[EUR][1000 genomes]
rs9493223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493226	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493227	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9493230	0.83[AMR][1000 genomes]
rs9493235	0.83[AMR][1000 genomes]
rs9632501	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762616	chr6:132404708-132584324	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6569775	C9orf16	trans	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132459600-132494800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:132486400-132509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:132487800-132491200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:132488800-132490000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:132488800-132490200	Enhancers	HepG2	liver
6	chr6:132488800-132490600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:132489000-132489600	Enhancers	Brain Angular Gyrus	brain
8	chr6:132489000-132489600	Enhancers	HUVEC	blood vessel
9	chr6:132489000-132489800	Enhancers	Brain Anterior Caudate	brain
10	chr6:132489000-132489800	Enhancers	NH-A	brain
11	chr6:132489000-132490000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:132489000-132490200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:132489000-132490200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:132489200-132489600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:132489200-132489600	Enhancers	Brain Hippocampus Middle	brain
16	chr6:132489200-132489600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr6:132489200-132489600	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:132489200-132489600	Enhancers	Small Intestine	intestine
19	chr6:132489200-132489800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:132489200-132490000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:132489200-132490000	Enhancers	Brain Cingulate Gyrus	brain
22	chr6:132489200-132490400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:132489400-132489600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr6:132489400-132489600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:132489400-132489600	Enhancers	Aorta	Aorta
26	chr6:132489400-132490000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:132489400-132490000	Enhancers	Brain Substantia Nigra	brain
28	chr6:132489400-132490200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr6:132489400-132490400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:132489400-132490400	Enhancers	Brain Germinal Matrix	brain

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