Variant report

Variant	rs12604538
Chromosome Location	chr18:12931789-12931790
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	chr18:12930468..12932965-chr18:12935532..12938033,2	K562	blood:
2	chr18:12924512..12926953-chr18:12930831..12933730,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11080617	0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs11080618	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs11660774	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11661908	0.82[JPT][hapmap]
rs11662766	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11664469	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12605189	0.87[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs12607398	1.00[JPT][hapmap]
rs12607919	0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12957380	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12960349	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs1523064	0.82[JPT][hapmap]
rs17603207	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs17659689	0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs17659896	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2282541	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs34166083	0.81[ASN][1000 genomes]
rs34765181	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35368962	0.81[ASN][1000 genomes]
rs3809914	0.81[ASN][1000 genomes]
rs3976787	0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs6505772	0.93[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs67768874	0.96[ASN][1000 genomes]
rs68004799	0.81[ASN][1000 genomes]
rs7228684	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs7229406	0.93[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7234619	0.87[MEX][hapmap]
rs7239486	0.85[ASN][1000 genomes]
rs8083393	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8088752	0.87[JPT][hapmap]
rs8090667	0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs8093236	0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs8093576	0.87[JPT][hapmap]
rs8096860	0.82[JPT][hapmap]
rs8566	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12604538	TWSG1	cis	cerebellum	SCAN
rs12604538	CEP192	cis	cerebellum	SCAN
rs12604538	CEP192	cis	parietal	SCAN
rs12604538	CEP192	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12922000-12933200	Weak transcription	Thymus	Thymus
2	chr18:12929000-12931800	Enhancers	Fetal Brain Male	brain
3	chr18:12929000-12935400	Enhancers	HepG2	liver
4	chr18:12929800-12934000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr18:12930000-12934400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr18:12930600-12932200	Weak transcription	Fetal Thymus	thymus

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