Variant report

Variant	rs730411
Chromosome Location	chr3:136700923-136700924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAG1-2	chr3:136700905-136701038	ENSG00000249407.1

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs6762370	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6762460	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6774347	1.00[AMR][1000 genomes]
rs72978802	1.00[AMR][1000 genomes]
rs748377	0.90[AFR][1000 genomes];1.00[AMR][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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136695400-136703600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:136695400-136706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:136698400-136703600	Weak transcription	Pancreas	Pancrea
4	chr3:136698800-136701000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:136698800-136701000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:136698800-136701400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:136698800-136702200	Weak transcription	Esophagus	oesophagus
8	chr3:136698800-136702200	Weak transcription	Hela-S3	cervix
9	chr3:136698800-136703600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:136698800-136703600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:136699000-136701600	Strong transcription	NHEK	skin
12	chr3:136699000-136703200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:136699000-136703400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:136699200-136701800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:136699800-136705400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:136700200-136703200	Weak transcription	Placenta	Placenta
17	chr3:136700400-136701200	Strong transcription	HMEC	breast
18	chr3:136700400-136701600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:136700400-136703600	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:136700600-136701000	Flanking Active TSS	Thymus	Thymus
21	chr3:136700600-136701200	Enhancers	Fetal Thymus	thymus
22	chr3:136700600-136701600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:136700600-136703400	Weak transcription	Left Ventricle	heart
24	chr3:136700800-136701000	Weak transcription	Right Ventricle	heart
25	chr3:136700800-136701400	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links