Variant report

Variant	rs9972405
Chromosome Location	chr15:45657374-45657375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10152337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152697	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324848	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288861	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16942066	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1706799	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17533116	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17533716	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17535381	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17537244	0.96[ASN][1000 genomes]
rs17618294	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433602	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453546	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2461706	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2486287	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668746	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55721266	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904415	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267974	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56273246	0.96[ASN][1000 genomes]
rs56306977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56327050	0.96[ASN][1000 genomes]
rs56937414	0.93[ASN][1000 genomes]
rs56967490	0.96[ASN][1000 genomes]
rs57369693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57419781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61301536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72709081	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709084	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709089	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72709092	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72711253	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711255	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711259	0.96[ASN][1000 genomes]
rs9972498	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9972405	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:66 , 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	chr15:45647600-45657800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:45647800-45661600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:45648200-45668600	Weak transcription	Colonic Mucosa	Colon
8	chr15:45648400-45664000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:45650000-45657800	Strong transcription	Brain Anterior Caudate	brain
10	chr15:45650000-45659000	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:45650000-45664200	Weak transcription	HSMMtube	muscle
12	chr15:45650200-45657600	Weak transcription	Aorta	Aorta
13	chr15:45650600-45668000	Weak transcription	Right Ventricle	heart
14	chr15:45650800-45662000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr15:45651600-45662000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr15:45651600-45665600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:45651800-45661000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:45652000-45658400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:45652000-45664400	Weak transcription	HSMM	muscle
20	chr15:45652200-45659400	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:45652400-45658400	Strong transcription	Colon Smooth Muscle	Colon
22	chr15:45652400-45663600	Weak transcription	Small Intestine	intestine
23	chr15:45652600-45668800	Weak transcription	Spleen	Spleen
24	chr15:45652800-45657400	Weak transcription	Fetal Brain Female	brain
25	chr15:45652800-45657600	Weak transcription	Esophagus	oesophagus
26	chr15:45652800-45669800	Weak transcription	Lung	lung
27	chr15:45653000-45667000	Weak transcription	Placenta	Placenta
28	chr15:45653400-45664200	Weak transcription	Stomach Mucosa	stomach
29	chr15:45653600-45663800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:45654000-45658600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:45654000-45659000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:45654000-45659000	Strong transcription	Adipose Nuclei	Adipose
33	chr15:45654000-45662400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr15:45654200-45658600	Strong transcription	GM12878-XiMat	blood
35	chr15:45654200-45666200	Genic enhancers	Liver	Liver
36	chr15:45654200-45668800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:45654600-45661800	Strong transcription	Fetal Intestine Large	intestine
38	chr15:45654800-45658000	Strong transcription	Fetal Stomach	stomach
39	chr15:45655000-45657800	Weak transcription	HepG2	liver
40	chr15:45655000-45658800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:45655000-45659600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr15:45655000-45663800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:45655200-45658600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr15:45655200-45668000	Weak transcription	Fetal Brain Male	brain
45	chr15:45655400-45657600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:45655400-45660800	Strong transcription	Fetal Intestine Small	intestine
47	chr15:45656000-45657600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:45656000-45657600	Genic enhancers	Brain Angular Gyrus	brain
49	chr15:45656000-45662200	Genic enhancers	Brain Substantia Nigra	brain
50	chr15:45656400-45658000	Genic enhancers	Pancreas	Pancrea

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