Variant report

Variant	rs2297475
Chromosome Location	chr10:90984623-90984624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11594137	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12415827	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12780342	0.86[CEU][hapmap]
rs17382301	1.00[JPT][hapmap]
rs2254636	0.86[CEU][hapmap]
rs4933497	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297475	LIPA	cis	Muscle Skeletal	GTEx

Chromatin state (count:114 , 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	chr10:90975600-90986800	Weak transcription	HepG2	liver
8	chr10:90975600-90994800	Weak transcription	Spleen	Spleen
9	chr10:90977200-90987400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr10:90977400-90999000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:90977400-90999200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:90977400-91010400	Weak transcription	Fetal Thymus	thymus
13	chr10:90977400-91010800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:90977600-90985200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr10:90977600-90986600	Weak transcription	A549	lung
16	chr10:90977600-90986600	Weak transcription	HSMM	muscle
17	chr10:90977600-90987000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr10:90977600-90994600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:90977600-90998600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:90977600-90998600	Weak transcription	NH-A	brain
21	chr10:90977600-90998800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr10:90977600-90998800	Weak transcription	Dnd41	blood
23	chr10:90977600-90999000	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:90977600-90999400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr10:90977600-90999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr10:90977600-91000600	Weak transcription	GM12878-XiMat	blood
27	chr10:90977600-91002000	Weak transcription	Hela-S3	cervix
28	chr10:90977600-91002000	Weak transcription	HSMMtube	muscle
29	chr10:90977600-91008800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:90977600-91009400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr10:90977600-91010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr10:90977600-91010800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr10:90978200-90998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:90978400-90988200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr10:90979000-90992200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr10:90979400-91003600	Strong transcription	Primary T cells from cord blood	blood
37	chr10:90979600-90985200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:90979800-90985000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr10:90980000-90985400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr10:90980000-90986800	Weak transcription	NHEK	skin
41	chr10:90980000-90990000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:90980000-90994000	Weak transcription	Esophagus	oesophagus
43	chr10:90980000-90995000	Weak transcription	Fetal Heart	heart
44	chr10:90980200-90999200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:90980600-90992800	Weak transcription	Fetal Stomach	stomach
46	chr10:90980800-90984800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:90980800-90984800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr10:90981000-90987600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr10:90981000-90993800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr10:90981200-90985000	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links