Variant report

Variant	rs12966203
Chromosome Location	chr18:24575498-24575499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:24574463..24577146-chr18:24577247..24578836,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10502482	1.00[ASN][1000 genomes]
rs12455253	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12458362	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12953982	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12954200	0.89[ASN][1000 genomes]
rs12956514	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12963112	0.87[ASN][1000 genomes]
rs12965711	0.87[ASN][1000 genomes]
rs12966301	0.99[ASN][1000 genomes]
rs12968314	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1436902	0.95[ASN][1000 genomes]
rs1436906	0.96[ASN][1000 genomes]
rs16943002	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16943003	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16943019	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16943023	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16943028	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16943030	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16943033	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16943045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16943049	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs16943089	0.92[ASN][1000 genomes]
rs16943144	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943156	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943160	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943161	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943164	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943175	0.99[ASN][1000 genomes]
rs16943178	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16943184	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16960687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821789	0.92[ASN][1000 genomes]
rs1941113	1.00[ASN][1000 genomes]
rs28564652	0.92[ASN][1000 genomes]
rs28647464	0.87[ASN][1000 genomes]
rs34738073	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35269358	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35443853	0.92[AFR][1000 genomes]
rs35507377	0.90[ASN][1000 genomes]
rs35871650	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3865412	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3893013	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4800273	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4800274	0.91[ASN][1000 genomes]
rs4800775	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4800776	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4800777	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4800782	0.92[AFR][1000 genomes]
rs56218423	0.92[ASN][1000 genomes]
rs60742277	0.92[ASN][1000 genomes]
rs60856601	0.92[ASN][1000 genomes]
rs6508462	0.92[ASN][1000 genomes]
rs71353414	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71353415	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71353416	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71353417	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71353424	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs71370779	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs717284	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7229046	0.92[ASN][1000 genomes]
rs7234761	1.00[ASN][1000 genomes]
rs7236637	0.92[ASN][1000 genomes]
rs8087494	0.92[ASN][1000 genomes]
rs9946779	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9948561	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9950360	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9957444	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1067103	chr18:24524011-24760469	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv543668	chr18:24524011-24760469	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12966203	C18orf16	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24545600-24590400	Weak transcription	Pancreas	Pancrea
2	chr18:24570000-24579200	Weak transcription	Fetal Intestine Small	intestine
3	chr18:24570400-24576200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr18:24570400-24598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr18:24571400-24582400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr18:24571600-24581200	Weak transcription	Ovary	ovary

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