Variant report

Variant	rs1153857
Chromosome Location	chr15:45659095-45659096
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1049518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145089	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145097	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1153845	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1153855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153860	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153862	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636114	0.88[AMR][1000 genomes]
rs11855414	0.90[AMR][1000 genomes]
rs12909409	0.90[AMR][1000 genomes]
rs12910764	0.90[AMR][1000 genomes]
rs1346267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1426932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547487	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1617634	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1617984	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1719245	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1719246	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2002035	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2015295	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2433601	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2433616	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2453533	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461700	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467853	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467865	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899375	0.88[AMR][1000 genomes]
rs35861938	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872192	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9921008	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1153857	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs1153857	CTD-2651B20.3	cis	lung	GTEx
rs1153857	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs1153857	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs1153857	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs1153857	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs1153857	CTD-2651B20.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1153857	CTD-2651B20.3	cis	Thyroid	GTEx
rs1153857	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs1153857	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs1153857	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs1153857	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs1153857	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs1153857	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45639200-45664200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:45639600-45661800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:45640600-45664200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:45640800-45664200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:45647800-45661600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:45648200-45668600	Weak transcription	Colonic Mucosa	Colon
7	chr15:45648400-45664000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:45650000-45664200	Weak transcription	HSMMtube	muscle
9	chr15:45650600-45668000	Weak transcription	Right Ventricle	heart
10	chr15:45650800-45662000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr15:45651600-45662000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr15:45651600-45665600	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:45651800-45661000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:45652000-45664400	Weak transcription	HSMM	muscle
15	chr15:45652200-45659400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:45652400-45663600	Weak transcription	Small Intestine	intestine
17	chr15:45652600-45668800	Weak transcription	Spleen	Spleen
18	chr15:45652800-45669800	Weak transcription	Lung	lung
19	chr15:45653000-45667000	Weak transcription	Placenta	Placenta
20	chr15:45653400-45664200	Weak transcription	Stomach Mucosa	stomach
21	chr15:45653600-45663800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:45654000-45662400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:45654200-45666200	Genic enhancers	Liver	Liver
24	chr15:45654200-45668800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:45654600-45661800	Strong transcription	Fetal Intestine Large	intestine
26	chr15:45655000-45659600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr15:45655000-45663800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:45655200-45668000	Weak transcription	Fetal Brain Male	brain
29	chr15:45655400-45660800	Strong transcription	Fetal Intestine Small	intestine
30	chr15:45656000-45662200	Genic enhancers	Brain Substantia Nigra	brain
31	chr15:45656400-45662200	Genic enhancers	Brain Hippocampus Middle	brain
32	chr15:45656400-45664000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:45656400-45668400	Weak transcription	Psoas Muscle	Psoas
34	chr15:45656600-45664600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:45656800-45659200	Strong transcription	Fetal Muscle Leg	muscle
36	chr15:45656800-45664200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:45657000-45660600	Weak transcription	Fetal Heart	heart
38	chr15:45657000-45663600	Weak transcription	Brain Germinal Matrix	brain
39	chr15:45657600-45664000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:45657800-45662800	Genic enhancers	Brain Anterior Caudate	brain
41	chr15:45658000-45659200	Strong transcription	Pancreas	Pancrea
42	chr15:45658000-45660200	Weak transcription	Fetal Stomach	stomach
43	chr15:45658400-45660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:45658400-45662800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:45658400-45663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:45658400-45663800	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:45658400-45664600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr15:45658400-45664600	Weak transcription	HepG2	liver
49	chr15:45658400-45664800	Weak transcription	Fetal Brain Female	brain
50	chr15:45658400-45665000	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links