Variant report

Variant	rs12549776
Chromosome Location	chr8:60195454-60195455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SDCBP-5	chr8:60195449-60196075	l_3606_chr8:60194334-60196450_lymphNode

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10104234	0.90[ASN][1000 genomes]
rs28581972	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28660971	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4131421	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4237031	0.92[ASN][1000 genomes]
rs4737540	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6989377	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831328	chr8:60062971-60288276	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1029441	chr8:60099776-60539141	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv539629	chr8:60099776-60539141	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831329	chr8:60162977-60356031	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:60191200-60196200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:60191400-60196200	Weak transcription	NHEK	skin
3	chr8:60191600-60196200	Weak transcription	HMEC	breast
4	chr8:60194600-60195600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr8:60194600-60196200	Enhancers	Primary hematopoietic stem cells	blood
6	chr8:60195000-60195600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr8:60195000-60195800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr8:60195000-60196600	Enhancers	Rectal Smooth Muscle	rectum
9	chr8:60195200-60195600	Enhancers	Primary B cells from peripheral blood	blood
10	chr8:60195200-60195600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr8:60195200-60195600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr8:60195200-60195600	Flanking Active TSS	Fetal Brain Male	brain
13	chr8:60195200-60195600	Enhancers	GM12878-XiMat	blood
14	chr8:60195200-60195800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:60195200-60195800	Flanking Active TSS	Fetal Brain Female	brain
16	chr8:60195200-60196000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:60195200-60196200	Enhancers	Fetal Heart	heart
18	chr8:60195200-60196200	Enhancers	Fetal Lung	lung
19	chr8:60195200-60196400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:60195200-60196400	Active TSS	Stomach Smooth Muscle	stomach
21	chr8:60195200-60196600	Enhancers	Adipose Nuclei	Adipose
22	chr8:60195200-60197600	Enhancers	Fetal Stomach	stomach
23	chr8:60195400-60195800	Active TSS	Colon Smooth Muscle	Colon
24	chr8:60195400-60196200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links