Variant report

Variant	rs1249630
Chromosome Location	chr18:11837556-11837557
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	chr18:11835732..11838374-chr18:11839010..11841922,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1249624	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12607581	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12607811	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1614379	0.81[CEU][hapmap]
rs1647558	0.81[CEU][hapmap]
rs1647561	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16976735	0.81[CHD][hapmap]
rs16976739	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs16976750	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs1786564	0.81[CEU][hapmap]
rs1786566	0.81[CEU][hapmap]
rs1786567	0.81[CEU][hapmap]
rs1786569	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1786570	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1786573	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276134	0.82[ASN][1000 genomes]
rs4324196	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56206349	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72868655	0.83[ASN][1000 genomes]
rs72868658	0.83[ASN][1000 genomes]
rs9962908	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs9966733	1.00[CEU][hapmap];0.81[CHB][hapmap]

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	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833590	chr18:11757329-11924539	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1249630	GNAL	cis	parietal	SCAN
rs1249630	C18orf1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11825400-11849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr18:11830800-11839600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:11830800-11849000	Weak transcription	A549	lung
4	chr18:11831800-11842600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr18:11835200-11840000	Weak transcription	Fetal Heart	heart
6	chr18:11836000-11839600	Weak transcription	HepG2	liver
7	chr18:11837400-11849200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:11837400-11849200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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