Variant report

Variant	rs12780342
Chromosome Location	chr10:90981876-90981877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11594137	0.89[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.85[EUR][1000 genomes]
rs12246667	1.00[JPT][hapmap]
rs17382301	0.82[CHD][hapmap]
rs2254636	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2297475	0.86[CEU][hapmap]
rs3802656	1.00[JPT][hapmap]
rs4933497	0.90[CHD][hapmap]
rs7077817	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7908760	1.00[JPT][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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1038123	chr10:90954417-90992129	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12780342	LIPA	cis	Muscle Skeletal	GTEx
rs12780342	PAPSS2	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90967600-90987200	Weak transcription	Aorta	Aorta
2	chr10:90968200-90983400	Weak transcription	NHLF	lung
3	chr10:90968200-90994800	Weak transcription	Gastric	stomach
4	chr10:90968400-90987200	Weak transcription	Pancreas	Pancrea
5	chr10:90968400-91000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:90968400-91002200	Weak transcription	Right Ventricle	heart
7	chr10:90970800-90984600	Weak transcription	Fetal Brain Female	brain
8	chr10:90971400-90984600	Weak transcription	Fetal Brain Male	brain
9	chr10:90973600-91001000	Weak transcription	Small Intestine	intestine
10	chr10:90974000-90984400	Weak transcription	Thymus	Thymus
11	chr10:90975600-90986800	Weak transcription	HepG2	liver
12	chr10:90975600-90994800	Weak transcription	Spleen	Spleen
13	chr10:90976800-90982400	Enhancers	Liver	Liver
14	chr10:90977200-90987400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:90977400-90983200	Weak transcription	Primary B cells from cord blood	blood
16	chr10:90977400-90999000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:90977400-90999200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:90977400-91010400	Weak transcription	Fetal Thymus	thymus
19	chr10:90977400-91010800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:90977600-90982200	Weak transcription	Fetal Lung	lung
21	chr10:90977600-90983600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:90977600-90983600	Weak transcription	Osteobl	bone
23	chr10:90977600-90983800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:90977600-90984600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:90977600-90984600	Weak transcription	Brain Germinal Matrix	brain
26	chr10:90977600-90985200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr10:90977600-90986600	Weak transcription	A549	lung
28	chr10:90977600-90986600	Weak transcription	HSMM	muscle
29	chr10:90977600-90987000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr10:90977600-90994600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr10:90977600-90998600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr10:90977600-90998600	Weak transcription	NH-A	brain
33	chr10:90977600-90998800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr10:90977600-90998800	Weak transcription	Dnd41	blood
35	chr10:90977600-90999000	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:90977600-90999400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr10:90977600-90999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr10:90977600-91000600	Weak transcription	GM12878-XiMat	blood
39	chr10:90977600-91002000	Weak transcription	Hela-S3	cervix
40	chr10:90977600-91002000	Weak transcription	HSMMtube	muscle
41	chr10:90977600-91008800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:90977600-91009400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr10:90977600-91010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr10:90977600-91010800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr10:90978000-90984000	Weak transcription	Fetal Kidney	kidney
46	chr10:90978200-90984600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr10:90978200-90998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:90978400-90983600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:90978400-90984400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:90978400-90988200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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