Variant report

Variant	rs12542189
Chromosome Location	chr8:19465619-19465620
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	chr8:19459085..19461454-chr8:19465027..19467183,2	K562	blood:

Variant related genes	Relation type
ENSG00000147408	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4565470	0.82[YRI][hapmap]
rs4922070	0.85[TSI][hapmap]
rs62494468	0.87[ASN][1000 genomes]
rs6998022	0.88[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv890626	chr8:19383697-19483259	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv610754	chr8:19419494-19525294	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv610756	chr8:19434021-19471977	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	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
rs12542189	ZDHHC2	cis	cerebellum	SCAN
rs12542189	EGR3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19445600-19481400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:19456200-19479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr8:19457600-19472200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr8:19459400-19472000	Weak transcription	Primary T cells from cord blood	blood
5	chr8:19459400-19472200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr8:19460200-19467400	Weak transcription	Spleen	Spleen
7	chr8:19460200-19474200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:19460200-19474200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:19460400-19466200	Weak transcription	Brain Angular Gyrus	brain
10	chr8:19460400-19466600	Enhancers	Fetal Lung	lung
11	chr8:19463400-19473200	Enhancers	Primary B cells from peripheral blood	blood
12	chr8:19464000-19467000	Enhancers	Hela-S3	cervix
13	chr8:19464200-19472200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr8:19464200-19476400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr8:19464400-19466000	Enhancers	Fetal Muscle Leg	muscle
16	chr8:19464400-19466400	Enhancers	Ovary	ovary
17	chr8:19464600-19465800	Enhancers	Brain Cingulate Gyrus	brain
18	chr8:19464600-19466000	Enhancers	Fetal Brain Male	brain
19	chr8:19464600-19466000	Enhancers	Placenta	Placenta
20	chr8:19464600-19466000	Enhancers	Right Ventricle	heart
21	chr8:19464600-19466200	Enhancers	Fetal Stomach	stomach
22	chr8:19464600-19466400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:19464800-19465800	Enhancers	Brain Hippocampus Middle	brain
24	chr8:19464800-19466200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr8:19464800-19466600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr8:19464800-19466600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr8:19464800-19466800	Enhancers	Osteobl	bone
28	chr8:19464800-19467000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:19465000-19465800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr8:19465000-19465800	Enhancers	Brain Anterior Caudate	brain
31	chr8:19465000-19465800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr8:19465000-19466000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr8:19465000-19466000	Enhancers	Esophagus	oesophagus
34	chr8:19465000-19466000	Enhancers	Left Ventricle	heart
35	chr8:19465000-19466400	Enhancers	NHDF-Ad	bronchial
36	chr8:19465000-19466600	Enhancers	Aorta	Aorta
37	chr8:19465000-19466600	Enhancers	NHLF	lung
38	chr8:19465200-19466000	Weak transcription	Adipose Nuclei	Adipose
39	chr8:19465200-19466200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr8:19465200-19466600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr8:19465200-19466600	Flanking Active TSS	A549	lung
42	chr8:19465400-19465800	Enhancers	Fetal Brain Female	brain
43	chr8:19465400-19468000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr8:19465600-19466000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr8:19465600-19466000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr8:19465600-19466000	Enhancers	Gastric	stomach
47	chr8:19465600-19466000	Enhancers	Pancreas	Pancrea
48	chr8:19465600-19466000	Enhancers	Right Atrium	heart
49	chr8:19465600-19466600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr8:19465600-19466800	Weak transcription	Primary B cells from cord blood	blood

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