Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr12:40549674-40549874	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRK2-1	chr12:40549559-40550164	NONHSAT027720

Variant related genes	Relation type
ENSG00000223914	TF binding region

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11564134	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11564154	1.00[CEU][hapmap]
rs11564163	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11564174	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11564186	1.00[CEU][hapmap]
rs11564188	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11564195	1.00[AFR][1000 genomes]
rs11564208	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17519173	1.00[CEU][hapmap]
rs17519531	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs17519580	1.00[CEU][hapmap]
rs2254475	1.00[CEU][hapmap]
rs28365208	1.00[CEU][hapmap]
rs28370698	1.00[CEU][hapmap]
rs73092794	0.94[AFR][1000 genomes]
rs73092800	0.94[AFR][1000 genomes]
rs73105433	0.88[AFR][1000 genomes]
rs73105445	1.00[AFR][1000 genomes]
rs73105478	1.00[AFR][1000 genomes]
rs73105482	1.00[AFR][1000 genomes]
rs73107664	1.00[AFR][1000 genomes]
rs73107677	1.00[AFR][1000 genomes]
rs7315719	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7315853	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7316047	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7966059	1.00[AFR][1000 genomes]
rs7974320	1.00[CEU][hapmap];1.00[YRI][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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40547200-40558600	Weak transcription	Liver	Liver
2	chr12:40547600-40551800	Weak transcription	NHEK	skin
3	chr12:40547800-40551200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40547800-40551200	Weak transcription	HMEC	breast
5	chr12:40547800-40551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:40547800-40552200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:40548000-40549800	Weak transcription	Primary B cells from cord blood	blood
8	chr12:40548400-40549800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:40548400-40551200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:40548600-40550200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:40548800-40553800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:40549200-40549800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr12:40549200-40550200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:40549400-40550000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:40549600-40549800	Enhancers	GM12878-XiMat	blood
16	chr12:40549600-40550400	Enhancers	Primary B cells from peripheral blood	blood
17	chr12:40549600-40552200	Enhancers	Primary monocytes fromperipheralblood	blood

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