Variant report

Variant	rs9946779
Chromosome Location	chr18:24520756-24520757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12326470	0.83[ASN][1000 genomes]
rs12326646	0.83[ASN][1000 genomes]
rs12455253	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12458362	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956514	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12962943	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12966203	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12968314	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12970341	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16943002	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943003	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943019	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943023	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943028	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16943030	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16943033	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16943045	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16943049	0.91[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16943144	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16943156	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16943160	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16943161	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16943164	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16960687	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35269358	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35871650	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3865412	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893013	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3916234	0.83[ASN][1000 genomes]
rs4800273	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4800775	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4800776	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4800777	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71353414	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353415	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353416	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71353417	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71370779	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9948561	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950196	0.82[ASN][1000 genomes]
rs9950360	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9957444	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv833600	chr18:24473894-24681019	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv909472	chr18:24479960-24614192	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9946779	C18orf16	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24503200-24520800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr18:24505400-24527200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr18:24508400-24529000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:24508600-24536800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr18:24518200-24522600	Weak transcription	Fetal Intestine Small	intestine
6	chr18:24518800-24521600	Weak transcription	Psoas Muscle	Psoas
7	chr18:24520200-24521000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:24520400-24521200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr18:24520600-24521200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr18:24520600-24521400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr18:24520600-24521600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr18:24520600-24521800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr18:24520600-24521800	Enhancers	Rectal Smooth Muscle	rectum

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