Variant report

Variant	rs2254636
Chromosome Location	chr10:90987007-90987008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11203084	1.00[CHB][hapmap]
rs12246667	1.00[JPT][hapmap]
rs12415827	0.89[CEU][hapmap]
rs12780342	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2297475	0.86[CEU][hapmap]
rs3802656	1.00[JPT][hapmap]
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
rs2254636	LIPA	cis	Muscle Skeletal	GTEx
rs2254636	LIPA	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90967600-90987200	Weak transcription	Aorta	Aorta
2	chr10:90968200-90994800	Weak transcription	Gastric	stomach
3	chr10:90968400-90987200	Weak transcription	Pancreas	Pancrea
4	chr10:90968400-91000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:90968400-91002200	Weak transcription	Right Ventricle	heart
6	chr10:90973600-91001000	Weak transcription	Small Intestine	intestine
7	chr10:90975600-90994800	Weak transcription	Spleen	Spleen
8	chr10:90977200-90987400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:90977400-90999000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr10:90977400-90999200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:90977400-91010400	Weak transcription	Fetal Thymus	thymus
12	chr10:90977400-91010800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:90977600-90994600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:90977600-90998600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:90977600-90998600	Weak transcription	NH-A	brain
16	chr10:90977600-90998800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr10:90977600-90998800	Weak transcription	Dnd41	blood
18	chr10:90977600-90999000	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:90977600-90999400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr10:90977600-90999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:90977600-91000600	Weak transcription	GM12878-XiMat	blood
22	chr10:90977600-91002000	Weak transcription	Hela-S3	cervix
23	chr10:90977600-91002000	Weak transcription	HSMMtube	muscle
24	chr10:90977600-91008800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr10:90977600-91009400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:90977600-91010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:90977600-91010800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:90978200-90998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:90978400-90988200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr10:90979000-90992200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr10:90979400-91003600	Strong transcription	Primary T cells from cord blood	blood
32	chr10:90980000-90990000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:90980000-90994000	Weak transcription	Esophagus	oesophagus
34	chr10:90980000-90995000	Weak transcription	Fetal Heart	heart
35	chr10:90980200-90999200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:90980600-90992800	Weak transcription	Fetal Stomach	stomach
37	chr10:90981000-90987600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr10:90981000-90993800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr10:90982200-90987800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr10:90982200-90988000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:90982400-90987200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr10:90982400-90988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr10:90982400-90998800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:90983200-90988800	Strong transcription	Primary B cells from cord blood	blood
45	chr10:90983400-90994600	Weak transcription	Left Ventricle	heart
46	chr10:90983600-90988200	Strong transcription	Fetal Intestine Small	intestine
47	chr10:90984000-90999600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:90984600-90987200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:90984800-90988200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr10:90984800-90998200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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