Variant report

Variant	rs11043288
Chromosome Location	chr12:122451187-122451188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122450006..122452585-chr12:122472596..122474160,2	K562	blood:
2	chr12:122445744..122449221-chr12:122451078..122453446,3	K562	blood:
3	chr12:122445617..122452949-chr12:122456112..122461928,13	MCF-7	breast:
4	chr12:122065145..122067836-chr12:122450179..122451724,2	K562	blood:
5	chr12:122449991..122452263-chr12:122459578..122462455,2	K562	blood:
6	chr12:122450614..122453245-chr12:122454645..122456321,2	K562	blood:

Variant related genes	Relation type
ENSG00000110987	Chromatin interaction
ENSG00000255856	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10840630	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10840631	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10840632	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10840633	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10840637	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10840640	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10840641	0.84[AMR][1000 genomes]
rs10840644	0.81[AMR][1000 genomes]
rs11043220	1.00[YRI][hapmap]
rs11043223	1.00[CHD][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs11043225	1.00[ASN][1000 genomes]
rs11043233	1.00[ASN][1000 genomes]
rs11043243	1.00[YRI][hapmap]
rs11043244	1.00[ASN][1000 genomes]
rs11043246	1.00[ASN][1000 genomes]
rs11043251	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11043271	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11043278	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043280	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043294	0.86[AMR][1000 genomes]
rs1154514	1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs11612028	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1169070	1.00[ASN][1000 genomes]
rs1169071	1.00[ASN][1000 genomes]
rs11833399	1.00[CHD][hapmap]
rs12369331	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809676	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822369	1.00[ASN][1000 genomes]
rs12822775	0.83[AMR][1000 genomes]
rs12823194	1.00[ASN][1000 genomes]
rs12824593	1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12825161	1.00[ASN][1000 genomes]
rs12827036	1.00[ASW][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs12830351	0.86[AMR][1000 genomes]
rs1720033	1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs1720037	1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs2167067	1.00[ASN][1000 genomes]
rs34159444	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906460	1.00[ASN][1000 genomes]
rs3847694	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs66751701	1.00[ASN][1000 genomes]
rs7132055	1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs7137218	0.84[TSI][hapmap]
rs7298990	0.86[AMR][1000 genomes]
rs73217776	1.00[ASN][1000 genomes]
rs7954584	0.82[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs9739381	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11043288	GPR109B	cis	parietal	SCAN
rs11043288	NCRNA00173	cis	cerebellum	SCAN
rs11043288	BCL7A	cis	Muscle Skeletal	GTEx
rs11043288	CCDC60	cis	cerebellum	SCAN
rs11043288	WDR66	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122442600-122458800	Weak transcription	Aorta	Aorta
2	chr12:122443000-122458800	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122443400-122458800	Weak transcription	Right Ventricle	heart
4	chr12:122443400-122459000	Weak transcription	Right Atrium	heart
5	chr12:122444600-122458600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:122446000-122451400	Weak transcription	Dnd41	blood
7	chr12:122448800-122451400	Weak transcription	Thymus	Thymus
8	chr12:122448800-122452200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:122449000-122451600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:122449000-122456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:122449800-122452400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:122450000-122451400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:122450400-122451400	Weak transcription	Fetal Thymus	thymus

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