Variant report

Variant	rs4306472
Chromosome Location	chr15:40912611-40912612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40912062..40914734-chr15:40918334..40921407,3	K562	blood:
2	chr15:40904218..40906885-chr15:40912001..40913717,2	K562	blood:
3	chr15:40910551..40912670-chr15:40914146..40915843,2	K562	blood:

Variant related genes	Relation type
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10400825	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10744948	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070284	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638204	0.82[EUR][1000 genomes]
rs11854763	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12438955	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592882	0.82[ASN][1000 genomes]
rs12708401	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899600	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906095	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12911738	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912058	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912339	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915109	0.82[EUR][1000 genomes]
rs12916082	0.82[EUR][1000 genomes]
rs1901775	0.80[ASN][1000 genomes]
rs2412541	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619681	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3092978	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34285050	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4417527	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4420508	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45457497	0.81[ASN][1000 genomes]
rs4924484	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924487	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924488	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924491	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924500	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6492957	0.85[EUR][1000 genomes]
rs6492958	0.85[EUR][1000 genomes]
rs66885559	0.82[ASN][1000 genomes]
rs7161938	0.85[EUR][1000 genomes]
rs7161968	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164289	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167417	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7167768	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7168873	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7171260	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171945	0.81[ASN][1000 genomes]
rs7172947	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7176221	0.87[ASN][1000 genomes]
rs7176974	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7177192	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178486	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8031057	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035775	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037417	0.81[ASN][1000 genomes]
rs8037804	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040502	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8041095	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8041443	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs936580	0.91[EUR][1000 genomes]
rs9806221	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv1843830	chr15:40902453-40915045	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4306472	RMDN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
2	chr15:40887800-40933200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
4	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:40888200-40912800	Weak transcription	HMEC	breast
8	chr15:40888400-40913200	Weak transcription	NHDF-Ad	bronchial
9	chr15:40888400-40913600	Weak transcription	NHLF	lung
10	chr15:40888400-40923200	Weak transcription	Osteobl	bone
11	chr15:40888400-40925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:40890800-40925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:40893600-40922600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:40899400-40922600	Weak transcription	Fetal Intestine Small	intestine
17	chr15:40899600-40913200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:40900000-40943600	Weak transcription	NH-A	brain
19	chr15:40900200-40912800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:40900400-40913200	Weak transcription	NHEK	skin
21	chr15:40900600-40912800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:40902200-40920400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:40902800-40913000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:40903000-40913000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:40903000-40922200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
27	chr15:40903200-40912800	Weak transcription	HUVEC	blood vessel
28	chr15:40903600-40912800	Weak transcription	GM12878-XiMat	blood
29	chr15:40903600-40913200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:40903600-40922600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:40903600-40927800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
35	chr15:40904800-40927800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:40905600-40912800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:40906400-40930200	Strong transcription	Dnd41	blood
38	chr15:40907000-40912800	Weak transcription	A549	lung
39	chr15:40908600-40917800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:40908800-40915000	Strong transcription	Hela-S3	cervix
41	chr15:40910200-40925200	Weak transcription	Placenta	Placenta
42	chr15:40910400-40915600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:40910600-40914800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:40911000-40914800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:40911000-40914800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:40911000-40916200	Strong transcription	HSMM	muscle
47	chr15:40911200-40913400	Strong transcription	Thymus	Thymus
48	chr15:40911200-40914800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:40911200-40918000	Strong transcription	Fetal Thymus	thymus
50	chr15:40911400-40912800	Weak transcription	K562	blood

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