Variant report

Variant	rs2412541
Chromosome Location	chr15:40913840-40913841
allele	G/T
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	chr15:40907487..40910390-chr15:40913134..40917272,4	K562	blood:
3	chr15:40908832..40911175-chr15:40913134..40914934,3	K562	blood:

Variant related genes	Relation type
ENSG00000137812	Chromatin interaction
ENSG00000265814	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10400825	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10467972	0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs10744948	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070284	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070285	0.80[JPT][hapmap]
rs11070286	0.80[JPT][hapmap]
rs11070292	0.91[CEU][hapmap]
rs1142468	0.84[EUR][1000 genomes]
rs11561564	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11629680	0.83[EUR][1000 genomes]
rs11632370	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs11633367	0.83[EUR][1000 genomes]
rs11638204	0.89[EUR][1000 genomes]
rs11638742	0.80[JPT][hapmap]
rs11852694	0.80[JPT][hapmap]
rs11854763	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854986	0.80[JPT][hapmap]
rs11855334	0.80[JPT][hapmap]
rs11856438	0.80[JPT][hapmap]
rs11858113	0.80[JPT][hapmap]
rs12438955	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440468	0.85[EUR][1000 genomes]
rs12592882	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12595610	0.80[JPT][hapmap]
rs12708401	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12899600	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906095	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12911738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912339	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914743	0.80[JPT][hapmap]
rs12915109	0.89[EUR][1000 genomes]
rs12916082	0.89[EUR][1000 genomes]
rs16970851	0.80[JPT][hapmap]
rs17747351	1.00[CEU][hapmap]
rs1901775	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278888	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs2304580	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2412531	0.80[JPT][hapmap];0.82[YRI][hapmap]
rs2412532	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2412544	0.80[JPT][hapmap]
rs2619681	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2924388	0.80[JPT][hapmap]
rs3092978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092979	0.83[CHB][hapmap]
rs34285050	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35047458	0.80[JPT][hapmap]
rs3751653	0.80[JPT][hapmap]
rs4306472	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4417527	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4420508	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4439732	0.85[EUR][1000 genomes]
rs45457497	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4923876	0.80[JPT][hapmap];0.82[YRI][hapmap]
rs4924478	0.80[JPT][hapmap]
rs4924481	0.80[JPT][hapmap]
rs4924484	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924487	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924490	0.83[EUR][1000 genomes]
rs4924491	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924500	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55640412	0.85[EUR][1000 genomes]
rs62019923	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62019924	0.80[AMR][1000 genomes]
rs62019925	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6492957	0.92[EUR][1000 genomes]
rs6492958	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs66885559	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7161938	1.00[CEU][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs7161968	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7162319	0.84[EUR][1000 genomes]
rs7162509	0.86[EUR][1000 genomes]
rs7164289	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7167417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7167768	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7168873	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7171260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7171945	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172947	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175361	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7176221	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176974	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178486	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025008	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8026605	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs8028999	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs8029384	0.80[JPT][hapmap]
rs8031057	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037417	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8037804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8040502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041095	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8041443	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8042729	0.91[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs896795	0.81[CHB][hapmap]
rs896796	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs936580	0.95[EUR][1000 genomes]
rs9806221	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2412541	RMDN3	cis	Heart Left Ventricle	GTEx
rs2412541	RMDN3	cis	Muscle Skeletal	GTEx
rs2412541	FAM82A2	cis	parietal	SCAN
rs2412541	TGFBR3	trans	lymphoblastoid	seeQTL
rs2412541	C15orf57	cis	lymphoblastoid	seeQTL
rs2412541	ZFYVE19	cis	cerebellum	SCAN
rs2412541	PLA2G4D	cis	parietal	SCAN

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	chr15:40888400-40923200	Weak transcription	Osteobl	bone
8	chr15:40888400-40925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:40890800-40925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:40893600-40922600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40899400-40922600	Weak transcription	Fetal Intestine Small	intestine
14	chr15:40900000-40943600	Weak transcription	NH-A	brain
15	chr15:40902200-40920400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:40903000-40922200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
18	chr15:40903600-40922600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:40903600-40927800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
23	chr15:40904800-40927800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:40906400-40930200	Strong transcription	Dnd41	blood
25	chr15:40908600-40917800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:40908800-40915000	Strong transcription	Hela-S3	cervix
27	chr15:40910200-40925200	Weak transcription	Placenta	Placenta
28	chr15:40910400-40915600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:40910600-40914800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:40911000-40914800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:40911000-40914800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:40911000-40916200	Strong transcription	HSMM	muscle
33	chr15:40911200-40914800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:40911200-40918000	Strong transcription	Fetal Thymus	thymus
35	chr15:40911400-40922200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:40911400-40930600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:40911600-40914800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:40911800-40914800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:40911800-40915200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:40911800-40917800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr15:40912000-40914400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:40912200-40915800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:40912200-40917800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
45	chr15:40912400-40921800	Weak transcription	Fetal Stomach	stomach
46	chr15:40912600-40922200	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:40912600-40941400	Weak transcription	HepG2	liver
48	chr15:40912800-40914000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr15:40912800-40914200	Strong transcription	K562	blood
50	chr15:40912800-40914600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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