Variant report

Variant	rs12111569
Chromosome Location	chr6:25006711-25006712
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:2204848..2205398-chr6:25006636..25007430,2	NB4	blood:

Variant related genes	Relation type
ENSG00000206630	Chromatin interaction
ENSG00000260260	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11964330	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12110508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56772860	0.82[EUR][1000 genomes]
rs58272875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58446150	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58858607	0.82[EUR][1000 genomes]
rs59935869	0.82[EUR][1000 genomes]
rs60753079	0.82[EUR][1000 genomes]
rs73384104	0.82[EUR][1000 genomes]
rs73384131	0.82[EUR][1000 genomes]
rs73384137	0.82[EUR][1000 genomes]
rs73384148	0.82[EUR][1000 genomes]
rs73384155	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384158	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384159	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384162	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73384165	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73384168	1.00[EUR][1000 genomes]
rs73384170	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24992200-25006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:24995600-25006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:24997800-25016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:24998200-25006800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:24998200-25009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:25000600-25006800	Weak transcription	Lung	lung
7	chr6:25000600-25007800	Weak transcription	Spleen	Spleen
8	chr6:25003200-25006800	Weak transcription	Left Ventricle	heart
9	chr6:25003200-25006800	Weak transcription	Pancreas	Pancrea
10	chr6:25003200-25006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:25003200-25006800	Weak transcription	NHDF-Ad	bronchial
12	chr6:25003200-25007000	Weak transcription	Esophagus	oesophagus
13	chr6:25003200-25007000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:25003400-25006800	Weak transcription	Adipose Nuclei	Adipose
15	chr6:25003400-25007800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:25003800-25006800	Enhancers	Primary T cells from cord blood	blood
17	chr6:25004000-25006800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:25004200-25006800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:25004200-25007000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:25004200-25011200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:25004400-25006800	Enhancers	Primary hematopoietic stem cells	blood
22	chr6:25004400-25011800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:25004600-25006800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:25004600-25008000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:25004600-25008000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:25004800-25007000	Enhancers	Primary B cells from cord blood	blood
27	chr6:25004800-25008200	Enhancers	HMEC	breast
28	chr6:25005000-25006800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:25005000-25006800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:25005000-25007000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:25005000-25007000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:25005000-25007400	Weak transcription	Brain Substantia Nigra	brain
33	chr6:25005400-25006800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:25005400-25006800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:25005400-25006800	Weak transcription	Fetal Brain Male	brain
36	chr6:25005400-25006800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:25005600-25006800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:25005600-25006800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:25005600-25006800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:25005600-25006800	Weak transcription	Brain Angular Gyrus	brain
41	chr6:25005600-25006800	Weak transcription	Fetal Heart	heart
42	chr6:25005800-25006800	Weak transcription	Right Ventricle	heart
43	chr6:25005800-25007000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr6:25006000-25007000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:25006000-25007000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr6:25006000-25007600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:25006000-25008000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:25006000-25008000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr6:25006200-25007400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:25006200-25007800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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