Variant report

Variant	rs12907984
Chromosome Location	chr15:40897586-40897587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40891684..40893459-chr15:40895042..40898185,3	K562	blood:
2	chr15:40884637..40889853-chr15:40895293..40899936,6	K562	blood:
3	chr15:40892966..40895127-chr15:40895336..40897665,2	MCF-7	breast:
4	chr15:40884808..40888126-chr15:40896275..40900248,4	K562	blood:

Variant related genes	Relation type
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1051482	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10851396	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11070279	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11070280	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11852479	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855517	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11857247	0.81[EUR][1000 genomes]
rs12148185	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898552	0.80[AMR][1000 genomes]
rs12899408	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12906755	0.93[EUR][1000 genomes]
rs12907448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908114	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12908443	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908867	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12914501	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12915563	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12916323	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1453183	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17746659	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17747399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2123534	0.81[AMR][1000 genomes]
rs2412545	0.82[AMR][1000 genomes]
rs28798094	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34303240	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34750756	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35884042	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36094699	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3743146	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3803353	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4457966	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45592734	0.80[AMR][1000 genomes]
rs5030783	0.82[AMR][1000 genomes]
rs55954396	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56384845	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62018046	0.80[AMR][1000 genomes]
rs62018048	0.83[AMR][1000 genomes]
rs62018051	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62019866	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62019883	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62019934	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7162749	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7164385	0.82[EUR][1000 genomes]
rs7165054	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181909	0.82[EUR][1000 genomes]
rs72733469	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8025458	0.90[EUR][1000 genomes]
rs8028910	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8031427	0.82[AMR][1000 genomes]
rs8036938	0.90[EUR][1000 genomes]
rs8038396	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8042733	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9806410	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs12907984	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs12907984	CCDC32	cis	multi-tissue	Pritchard
rs12907984	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12907984	C15orf57	cis	Stomach	GTEx
rs12907984	C15orf57	cis	Esophagus Muscularis	GTEx
rs12907984	RP11-111A22.1	cis	lung	GTEx
rs12907984	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12907984	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12907984	C15orf57	cis	Esophagus Mucosa	GTEx
rs12907984	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12907984	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12907984	C15orf57	cis	Artery Aorta	GTEx
rs12907984	C15orf57	cis	Artery Tibial	GTEx
rs12907984	ZFYVE19	cis	multi-tissue	Pritchard
rs12907984	C15orf57	cis	Nerve Tibial	GTEx
rs12907984	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12907984	C15orf57	cis	lung	GTEx
rs12907984	RP11-111A22.1	cis	Stomach	GTEx
rs12907984	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs12907984	C15orf57	cis	Muscle Skeletal	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887200-40898800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:40887600-40898800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:40887600-40902600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
5	chr15:40887800-40898800	Weak transcription	Fetal Stomach	stomach
6	chr15:40887800-40902000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:40887800-40933200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
9	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:40888000-40897800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr15:40888000-40898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:40888000-40898600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:40888000-40899400	Weak transcription	HSMM	muscle
15	chr15:40888000-40901200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:40888000-40903400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:40888200-40897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:40888200-40898600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:40888200-40898800	Weak transcription	NH-A	brain
21	chr15:40888200-40902200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:40888200-40912800	Weak transcription	HMEC	breast
23	chr15:40888400-40897800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:40888400-40898000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:40888400-40898200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:40888400-40898800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:40888400-40898800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:40888400-40898800	Weak transcription	Fetal Intestine Small	intestine
29	chr15:40888400-40899800	Weak transcription	HUVEC	blood vessel
30	chr15:40888400-40900800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:40888400-40913200	Weak transcription	NHDF-Ad	bronchial
32	chr15:40888400-40913600	Weak transcription	NHLF	lung
33	chr15:40888400-40923200	Weak transcription	Osteobl	bone
34	chr15:40888400-40925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:40889600-40898000	Weak transcription	K562	blood
37	chr15:40889600-40901400	Weak transcription	HepG2	liver
38	chr15:40890800-40898000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:40890800-40899000	Weak transcription	NHEK	skin
40	chr15:40890800-40904800	Weak transcription	A549	lung
41	chr15:40890800-40925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:40893400-40898000	Weak transcription	GM12878-XiMat	blood
43	chr15:40893400-40907200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:40893600-40922600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:40895000-40903200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr15:40895200-40898800	Strong transcription	Hela-S3	cervix
47	chr15:40895800-40899600	Strong transcription	Thymus	Thymus
48	chr15:40895800-40905200	Strong transcription	Fetal Thymus	thymus
49	chr15:40895800-40905600	Strong transcription	Dnd41	blood
50	chr15:40896000-40910200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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