Variant report

Variant	rs11666662
Chromosome Location	chr19:38154702-38154703
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38145451..38150086-chr19:38150215..38155612,4	K562	blood:

Variant related genes	Relation type
ENSG00000120784	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11083427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11665759	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11666738	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11672440	0.87[CEU][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap]
rs12151280	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs12162238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12459013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460230	0.90[JPT][hapmap]
rs12462505	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1478462	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17303301	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17305326	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045911	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2126976	0.83[ASN][1000 genomes]
rs2279150	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2290999	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs241952	0.80[CEU][hapmap]
rs241955	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35205379	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[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848624	0.81[ASN][1000 genomes]
rs59426132	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60731897	0.81[ASN][1000 genomes]
rs7248397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73031309	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73031321	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73031322	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73031326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73033117	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73033129	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73033139	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73033145	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73035158	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73035164	0.98[EUR][1000 genomes]
rs73037036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039018	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11666662	PSMC4	cis	parietal	SCAN
rs11666662	CATSPERG	cis	parietal	SCAN
rs11666662	ZFP112	cis	parietal	SCAN
rs11666662	FOSB	cis	cerebellum	SCAN
rs11666662	MRPS12	cis	cerebellum	SCAN
rs11666662	KIAA0961	cis	multi-tissue	Pritchard
rs11666662	PLEKHG2	cis	cerebellum	SCAN
rs11666662	CEACAM19	cis	cerebellum	SCAN
rs11666662	EIF3K	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38147600-38155800	Weak transcription	Brain Germinal Matrix	brain
2	chr19:38147600-38156400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr19:38152000-38169000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:38153000-38155200	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr19:38153600-38154800	ZNF genes & repeats	Liver	Liver
6	chr19:38153600-38154800	ZNF genes & repeats	Brain Hippocampus Middle	brain
7	chr19:38153800-38154800	ZNF genes & repeats	Brain Anterior Caudate	brain
8	chr19:38153800-38155000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
9	chr19:38153800-38155400	ZNF genes & repeats	Aorta	Aorta

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