Variant report

Variant	rs8028759
Chromosome Location	chr15:58812199-58812200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58811000..58814506-chr15:58833587..58836863,3	K562	blood:
2	chr15:58805398..58807499-chr15:58809534..58812404,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166035	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12592017	0.86[CHB][hapmap]
rs1979177	0.81[CHB][hapmap]

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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv569601	chr15:58800766-58866156	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8028759	CGNL1	cis	cerebellum	SCAN
rs8028759	TCF12	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58798600-58813200	Weak transcription	Aorta	Aorta
2	chr15:58798800-58812600	Weak transcription	Left Ventricle	heart
3	chr15:58803800-58812600	Weak transcription	Esophagus	oesophagus
4	chr15:58804000-58816200	Weak transcription	Liver	Liver
5	chr15:58806200-58813200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:58806400-58812600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:58806400-58813200	Weak transcription	Pancreas	Pancrea
8	chr15:58807000-58812600	Enhancers	Primary T cells from cord blood	blood
9	chr15:58807000-58813400	Weak transcription	Fetal Brain Male	brain
10	chr15:58807600-58815400	Enhancers	Fetal Thymus	thymus
11	chr15:58807800-58812600	Enhancers	K562	blood
12	chr15:58807800-58813400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr15:58807800-58815800	Enhancers	Primary B cells from cord blood	blood
14	chr15:58807800-58820200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr15:58808400-58813600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:58808400-58816200	Weak transcription	HepG2	liver
17	chr15:58809000-58812600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:58809600-58813600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:58809600-58813600	Weak transcription	Stomach Mucosa	stomach
20	chr15:58809600-58814800	Enhancers	Fetal Stomach	stomach
21	chr15:58809600-58817000	Enhancers	Brain Substantia Nigra	brain
22	chr15:58810000-58813200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:58810000-58813600	Weak transcription	Brain Angular Gyrus	brain
24	chr15:58810200-58812400	Weak transcription	Fetal Muscle Leg	muscle
25	chr15:58810200-58813200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr15:58810200-58813400	Weak transcription	HSMMtube	muscle
27	chr15:58810400-58812600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:58810600-58812600	Weak transcription	Placenta	Placenta
29	chr15:58810800-58812600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:58810800-58812600	Weak transcription	Right Atrium	heart
31	chr15:58810800-58813000	Enhancers	Fetal Kidney	kidney
32	chr15:58811000-58812400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:58811000-58812400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr15:58811000-58812400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:58811000-58812400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr15:58811000-58812600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:58811000-58813600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:58811200-58812200	Weak transcription	Thymus	Thymus
39	chr15:58811200-58812600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:58811200-58815400	Enhancers	GM12878-XiMat	blood
41	chr15:58811400-58812400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:58811400-58813200	Enhancers	Fetal Lung	lung
43	chr15:58811600-58812200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr15:58811600-58813400	Enhancers	HUVEC	blood vessel
45	chr15:58811600-58815800	Enhancers	Brain Hippocampus Middle	brain
46	chr15:58811800-58812200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:58811800-58812600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr15:58811800-58812800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:58811800-58813200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:58811800-58813400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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