Variant report

Variant	rs11525712
Chromosome Location	chr2:99821528-99821529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10187854	0.80[AFR][1000 genomes]
rs11123769	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12993310	0.84[EUR][1000 genomes]
rs1487271	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1487272	0.83[AFR][1000 genomes]
rs1565054	0.82[EUR][1000 genomes]
rs1843807	0.84[EUR][1000 genomes]
rs35996174	0.85[AFR][1000 genomes]
rs4851189	0.82[EUR][1000 genomes]
rs4851191	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4851194	0.84[EUR][1000 genomes]
rs6542871	0.82[EUR][1000 genomes]
rs7579999	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7586635	0.85[AFR][1000 genomes]
rs7602401	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11525712	LYG1	cis	Whole Blood	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
3	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
4	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
5	chr2:99803800-99829600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:99807000-99832600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:99807600-99825000	Weak transcription	Stomach Mucosa	stomach
8	chr2:99814000-99834800	Weak transcription	Gastric	stomach
9	chr2:99814200-99823600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:99814200-99828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:99814200-99832400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:99814400-99842200	Weak transcription	Ovary	ovary
13	chr2:99814400-99842800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:99814800-99840600	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:99815000-99823000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:99815000-99829000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:99815000-99834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:99815000-99836400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:99815000-99840600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:99815000-99840800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:99815000-99841800	Weak transcription	Pancreas	Pancrea
22	chr2:99815000-99842400	Weak transcription	Fetal Lung	lung
23	chr2:99815200-99821600	Weak transcription	Fetal Intestine Small	intestine
24	chr2:99815200-99821800	Weak transcription	Placenta	Placenta
25	chr2:99815200-99827400	Weak transcription	HMEC	breast
26	chr2:99815200-99827600	Weak transcription	Brain Germinal Matrix	brain
27	chr2:99815200-99827600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:99815200-99830400	Weak transcription	Brain Anterior Caudate	brain
29	chr2:99815200-99833200	Weak transcription	Lung	lung
30	chr2:99815200-99838400	Weak transcription	Adipose Nuclei	Adipose
31	chr2:99815200-99840600	Weak transcription	Aorta	Aorta
32	chr2:99815200-99841800	Weak transcription	Spleen	Spleen
33	chr2:99815200-99842000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:99815200-99842400	Weak transcription	Brain Substantia Nigra	brain
35	chr2:99815400-99821600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:99815400-99834400	Weak transcription	NHEK	skin
37	chr2:99815400-99834600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:99815600-99834400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:99815600-99834800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:99815600-99842000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:99815600-99842200	Weak transcription	Fetal Stomach	stomach
42	chr2:99815600-99843400	Weak transcription	Fetal Brain Female	brain
43	chr2:99816200-99821800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:99818200-99821600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:99818200-99854600	Weak transcription	Left Ventricle	heart
46	chr2:99818400-99827600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:99818400-99830400	Weak transcription	A549	lung
48	chr2:99818400-99836400	Weak transcription	Brain Angular Gyrus	brain
49	chr2:99818600-99842200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:99818800-99821800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links