Variant report

Variant	rs12908867
Chromosome Location	chr15:40867456-40867457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40867311..40870142-chr15:40875469..40877107,2	K562	blood:
2	chr15:40866258..40868658-chr15:40873477..40876647,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1051482	0.85[EUR][1000 genomes]
rs10851396	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070280	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11852479	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11855517	0.83[EUR][1000 genomes]
rs11857247	0.86[EUR][1000 genomes]
rs12148185	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12899408	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12906755	0.87[EUR][1000 genomes]
rs12907448	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12907984	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12908114	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12908443	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12914501	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12915563	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916323	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1453183	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17746659	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17747399	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2123534	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28798094	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34303240	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34750756	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35884042	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36094699	0.83[EUR][1000 genomes]
rs3743146	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3803353	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4457966	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55954396	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56384845	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61048252	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018046	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62018048	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018051	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62019866	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62019883	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62019934	0.82[EUR][1000 genomes]
rs7162749	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7164385	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7165054	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181909	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72733469	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs731640	0.80[EUR][1000 genomes]
rs8025458	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8028910	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8036938	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8038396	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8042733	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9806410	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs12908867	C15orf57	cis	Esophagus Mucosa	GTEx
rs12908867	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12908867	C15orf57	cis	lung	GTEx
rs12908867	CCDC32	cis	multi-tissue	Pritchard
rs12908867	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs12908867	C15orf57	cis	Muscle Skeletal	GTEx
rs12908867	RP11-111A22.1	cis	Stomach	GTEx
rs12908867	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs12908867	C15orf57	cis	Artery Tibial	GTEx
rs12908867	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12908867	C15orf57	cis	Esophagus Muscularis	GTEx
rs12908867	C15orf57	cis	Artery Aorta	GTEx
rs12908867	C15orf57	cis	Nerve Tibial	GTEx
rs12908867	RP11-111A22.1	cis	lung	GTEx
rs12908867	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12908867	C15orf57	cis	Stomach	GTEx
rs12908867	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12908867	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12908867	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12908867	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12908867	ZFYVE19	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40862800-40875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:40863000-40868200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:40863000-40870200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:40863000-40875000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:40863000-40875000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:40863200-40868600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:40863200-40868800	Weak transcription	Fetal Heart	heart
8	chr15:40863200-40869000	Weak transcription	Fetal Brain Male	brain
9	chr15:40863600-40867600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:40863600-40867600	Strong transcription	Adipose Nuclei	Adipose
11	chr15:40863600-40867600	Strong transcription	Ovary	ovary
12	chr15:40863600-40867800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:40863600-40867800	Strong transcription	Brain Hippocampus Middle	brain
14	chr15:40863600-40868000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:40863600-40868000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:40863800-40867600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:40863800-40867600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:40863800-40867600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr15:40863800-40867600	Strong transcription	NHLF	lung
20	chr15:40863800-40867800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr15:40863800-40868000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:40863800-40868000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:40864000-40867600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:40864000-40868000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:40864000-40868800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:40864200-40867600	Strong transcription	Hela-S3	cervix
27	chr15:40864200-40867600	Strong transcription	K562	blood
28	chr15:40865400-40867600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:40865400-40867800	Strong transcription	Brain Germinal Matrix	brain
30	chr15:40865600-40868200	Strong transcription	Psoas Muscle	Psoas
31	chr15:40865800-40875000	Weak transcription	Fetal Lung	lung
32	chr15:40866000-40870000	Weak transcription	NH-A	brain
33	chr15:40866000-40874800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:40866400-40868200	Weak transcription	Small Intestine	intestine
35	chr15:40866400-40869000	Weak transcription	Fetal Kidney	kidney
36	chr15:40866400-40874800	Weak transcription	Colonic Mucosa	Colon
37	chr15:40866400-40876600	Weak transcription	HSMMtube	muscle
38	chr15:40866400-40878200	Weak transcription	Brain Angular Gyrus	brain
39	chr15:40866600-40867800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:40866600-40868400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:40866600-40868400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:40866600-40868400	Weak transcription	Aorta	Aorta
43	chr15:40866600-40868400	Weak transcription	Right Ventricle	heart
44	chr15:40866600-40868600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:40866600-40868600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:40866600-40868600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:40866600-40868800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:40866600-40869600	Weak transcription	Fetal Stomach	stomach
49	chr15:40866600-40870000	Weak transcription	Gastric	stomach
50	chr15:40866600-40870200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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