Variant report

Variant	rs7335056
Chromosome Location	chr13:39396088-39396089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STOML3-1	chr13:39395935-39396239	ENSG00000225350.1

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs3884530	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4400923	0.87[AFR][1000 genomes]
rs7325406	1.00[EUR][1000 genomes]
rs7327183	1.00[EUR][1000 genomes]
rs7328965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982164	0.94[AFR][1000 genomes]
rs7982333	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7982933	1.00[EUR][1000 genomes]
rs7983560	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576622	0.92[AFR][1000 genomes]
rs9576624	0.88[AFR][1000 genomes]
rs9594296	1.00[EUR][1000 genomes]
rs9603431	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603432	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603434	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9805487	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39389000-39397400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:39389200-39404800	Weak transcription	Gastric	stomach
3	chr13:39389400-39423000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr13:39392600-39397200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr13:39393200-39397600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:39393400-39396400	Enhancers	Rectal Smooth Muscle	rectum
7	chr13:39393600-39398800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr13:39393600-39400400	Weak transcription	Pancreas	Pancrea
9	chr13:39394600-39423000	Weak transcription	Fetal Kidney	kidney
10	chr13:39394800-39397600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:39394800-39397600	Enhancers	HMEC	breast
12	chr13:39395600-39396400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:39395600-39396800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr13:39395600-39397000	Enhancers	Brain Cingulate Gyrus	brain
15	chr13:39395600-39397000	Enhancers	Brain Hippocampus Middle	brain
16	chr13:39395600-39397000	Enhancers	NHEK	skin
17	chr13:39395800-39396200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:39395800-39396200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr13:39395800-39396400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr13:39395800-39396400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:39395800-39396400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:39395800-39396800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:39395800-39396800	Enhancers	Colon Smooth Muscle	Colon
24	chr13:39395800-39397000	Enhancers	Brain Substantia Nigra	brain
25	chr13:39395800-39397400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:39395800-39397600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr13:39395800-39397600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr13:39396000-39396200	Enhancers	Fetal Stomach	stomach
29	chr13:39396000-39396400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr13:39396000-39396400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:39396000-39396400	Weak transcription	Brain Angular Gyrus	brain
32	chr13:39396000-39396400	Weak transcription	Brain Anterior Caudate	brain
33	chr13:39396000-39396400	Enhancers	Fetal Heart	heart
34	chr13:39396000-39396800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr13:39396000-39397600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr13:39396000-39399600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links