Variant report

Variant	rs12899408
Chromosome Location	chr15:40874841-40874842
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	chr15:40866258..40868658-chr15:40873477..40876647,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1051482	0.85[EUR][1000 genomes]
rs10851396	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11070279	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070280	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11852479	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11855517	0.83[EUR][1000 genomes]
rs11857247	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12148185	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12906755	0.88[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]
rs12908114	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908443	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12908867	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12914501	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915563	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12916323	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1453183	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17746659	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17747399	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2123534	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28798094	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34303240	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34750756	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35884042	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36094699	0.84[EUR][1000 genomes]
rs3743146	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3803353	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4457966	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55954396	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56384845	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61048252	0.83[EUR][1000 genomes]
rs62018046	0.84[AMR][1000 genomes]
rs62018048	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62018051	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62019866	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62019883	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62019934	0.83[EUR][1000 genomes]
rs7162749	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7164385	0.86[EUR][1000 genomes]
rs7165054	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181909	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72733469	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8025458	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8028910	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8036938	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8038396	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8042733	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9806410	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs12899408	C15orf57	cis	Artery Aorta	GTEx
rs12899408	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12899408	C15orf57	cis	Esophagus Mucosa	GTEx
rs12899408	RP11-111A22.1	cis	Stomach	GTEx
rs12899408	C15orf57	cis	Nerve Tibial	GTEx
rs12899408	C15orf57	cis	Artery Tibial	GTEx
rs12899408	C15orf57	cis	Esophagus Muscularis	GTEx
rs12899408	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs12899408	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs12899408	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12899408	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12899408	CCDC32	cis	multi-tissue	Pritchard
rs12899408	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12899408	C15orf57	cis	Muscle Skeletal	GTEx
rs12899408	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12899408	C15orf57	cis	lung	GTEx
rs12899408	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12899408	RP11-111A22.1	cis	lung	GTEx
rs12899408	ZFYVE19	cis	multi-tissue	Pritchard
rs12899408	C15orf57	cis	Stomach	GTEx
rs12899408	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12899408	RP11-111A22.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40862800-40875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:40863000-40875000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:40863000-40875000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:40865800-40875000	Weak transcription	Fetal Lung	lung
5	chr15:40866400-40876600	Weak transcription	HSMMtube	muscle
6	chr15:40866400-40878200	Weak transcription	Brain Angular Gyrus	brain
7	chr15:40866600-40875000	Weak transcription	Lung	lung
8	chr15:40866600-40875000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:40866600-40875200	Weak transcription	Spleen	Spleen
10	chr15:40866600-40875200	Weak transcription	HSMM	muscle
11	chr15:40866600-40881800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:40866600-40881800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:40866600-40881800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:40866800-40875200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:40866800-40875200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:40866800-40875200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:40867000-40875200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:40867200-40875000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:40867200-40875000	Weak transcription	Primary B cells from cord blood	blood
20	chr15:40867200-40875000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:40867200-40875000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:40867200-40875000	Weak transcription	Brain Substantia Nigra	brain
23	chr15:40867200-40875000	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:40867200-40875000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:40867200-40875200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:40867200-40875200	Weak transcription	Fetal Thymus	thymus
27	chr15:40867200-40875200	Weak transcription	Left Ventricle	heart
28	chr15:40867200-40875200	Weak transcription	HMEC	breast
29	chr15:40867200-40876400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:40867400-40875000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:40867400-40875000	Weak transcription	Dnd41	blood
32	chr15:40867400-40875000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:40867400-40875200	Weak transcription	Fetal Intestine Large	intestine
34	chr15:40867400-40875200	Weak transcription	NHDF-Ad	bronchial
35	chr15:40867400-40875400	Weak transcription	NHEK	skin
36	chr15:40867400-40876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:40867400-40883600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:40867600-40875000	Weak transcription	Ovary	ovary
39	chr15:40867600-40875000	Weak transcription	K562	blood
40	chr15:40867600-40875200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:40867600-40875200	Weak transcription	NHLF	lung
42	chr15:40867800-40876400	Weak transcription	Brain Hippocampus Middle	brain
43	chr15:40868000-40875200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:40868200-40875200	Weak transcription	Psoas Muscle	Psoas
45	chr15:40874200-40876400	Active TSS	HepG2	liver
46	chr15:40874200-40876600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:40874800-40875000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:40874800-40875000	Flanking Active TSS	Liver	Liver
49	chr15:40874800-40875000	Enhancers	Placenta	Placenta
50	chr15:40874800-40875000	Flanking Active TSS	Hela-S3	cervix

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