Variant report

Variant	rs4775707
Chromosome Location	chr15:45327794-45327795
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11634731	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903829	0.81[ASN][1000 genomes]
rs2437866	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2467841	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2467843	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470686	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2854446	0.82[ASN][1000 genomes]
rs35628479	0.89[EUR][1000 genomes]
rs3874239	0.88[EUR][1000 genomes]
rs58232764	0.80[ASN][1000 genomes]
rs7165595	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7167120	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv977710	chr15:45316191-45360995	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv827318	chr15:45318881-45328666	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
8	esv3311761	chr15:45326620-45328570	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a
9	esv3311762	chr15:45326620-45328570	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4775707	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4775707	RP11-109D20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4775707	SORD	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45316200-45340600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:45316400-45329400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:45316400-45333000	Weak transcription	Lung	lung
4	chr15:45316400-45341200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:45316400-45342200	Weak transcription	HSMMtube	muscle
6	chr15:45316400-45342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:45316600-45328800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr15:45316600-45328800	Weak transcription	Pancreas	Pancrea
9	chr15:45316600-45329000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:45316600-45329000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:45316600-45329000	Weak transcription	Osteobl	bone
12	chr15:45316600-45329200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:45316600-45329200	Weak transcription	NHLF	lung
14	chr15:45316600-45329400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:45316600-45329600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:45316600-45339200	Weak transcription	Fetal Lung	lung
17	chr15:45316600-45340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:45316600-45340600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:45316600-45340600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:45316600-45344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:45316600-45351000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:45316600-45356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:45316600-45366600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:45316800-45337600	Weak transcription	GM12878-XiMat	blood
25	chr15:45316800-45340600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:45316800-45346400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:45319200-45363200	Weak transcription	Fetal Thymus	thymus
28	chr15:45319400-45329000	Weak transcription	A549	lung
29	chr15:45319600-45329000	Weak transcription	Brain Anterior Caudate	brain
30	chr15:45319800-45329000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:45319800-45339800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:45319800-45340600	Weak transcription	Right Ventricle	heart
33	chr15:45319800-45363600	Weak transcription	Brain Angular Gyrus	brain
34	chr15:45320200-45328800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:45320400-45329000	Weak transcription	Fetal Heart	heart
36	chr15:45322000-45339600	Weak transcription	Ovary	ovary
37	chr15:45322000-45340600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:45322000-45340600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:45322000-45340600	Weak transcription	Primary T cells from cord blood	blood
40	chr15:45322000-45341000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:45322200-45328600	Weak transcription	HepG2	liver
42	chr15:45322200-45329000	Weak transcription	Brain Substantia Nigra	brain
43	chr15:45322200-45339600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:45322200-45339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:45322400-45335200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:45322600-45340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:45322600-45340600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:45323400-45340000	Weak transcription	NHEK	skin
49	chr15:45323600-45328000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:45323600-45329200	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links