Variant report

Variant	rs4410047
Chromosome Location	chr15:40944781-40944782
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40888439..40890299-chr15:40942541..40945027,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1037445	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10400890	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10400901	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10444817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070282	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070285	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070286	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632061	0.86[EUR][1000 genomes]
rs11632370	0.86[EUR][1000 genomes]
rs11852670	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852694	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852828	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854986	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855334	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855923	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856802	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11858113	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11858938	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591207	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902568	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904801	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905162	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912635	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913697	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12914743	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16970851	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1813898	0.86[EUR][1000 genomes]
rs1967368	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2412531	0.86[EUR][1000 genomes]
rs2412532	0.86[EUR][1000 genomes]
rs2412544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898996	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2924387	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3092979	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34845954	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35047458	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751652	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751653	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4080706	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4923876	0.86[EUR][1000 genomes]
rs4924481	0.86[EUR][1000 genomes]
rs62019916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62019918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582	0.86[EUR][1000 genomes]
rs71471881	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7169621	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7181074	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182530	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026605	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8029384	0.86[EUR][1000 genomes]
rs8034043	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8034048	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036737	0.90[EUR][1000 genomes]
rs8038407	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8041534	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs896795	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs4410047	RP11-111A22.1	cis	Artery Tibial	GTEx
rs4410047	C15orf57	cis	Adipose Subcutaneous	GTEx
rs4410047	C15orf57	cis	Muscle Skeletal	GTEx
rs4410047	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs4410047	RP11-111A22.1	cis	lung	GTEx
rs4410047	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs4410047	CCDC32	cis	multi-tissue	Pritchard
rs4410047	C15orf57	cis	Artery Aorta	GTEx
rs4410047	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs4410047	RP11-111A22.1	cis	Stomach	GTEx
rs4410047	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs4410047	RP11-111A22.1	cis	Artery Aorta	GTEx
rs4410047	C15orf57	cis	Thyroid	GTEx
rs4410047	C15orf57	cis	Artery Tibial	GTEx
rs4410047	ZFYVE19	cis	multi-tissue	Pritchard
rs4410047	C15orf57	cis	lung	GTEx
rs4410047	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs4410047	C15orf57	cis	Stomach	GTEx
rs4410047	C15orf57	cis	Esophagus Muscularis	GTEx
rs4410047	C15orf57	cis	Heart Left Ventricle	GTEx
rs4410047	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs4410047	C15orf57	cis	Esophagus Mucosa	GTEx
rs4410047	C15orf57	cis	Nerve Tibial	GTEx
rs4410047	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
6	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
9	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
10	chr15:40913800-40986000	Weak transcription	A549	lung
11	chr15:40914400-40960000	Weak transcription	NHLF	lung
12	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
14	chr15:40919800-40950200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:40922800-40954200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:40923000-40954400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:40923200-40947000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:40924000-40956600	Weak transcription	Fetal Brain Female	brain
20	chr15:40925000-40956200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:40925400-40956000	Weak transcription	Brain Germinal Matrix	brain
22	chr15:40926000-40947200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:40928200-40949400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:40928200-40951200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:40928600-40945600	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:40932600-40946800	Weak transcription	Fetal Stomach	stomach
29	chr15:40934200-40945000	Weak transcription	HSMM	muscle
30	chr15:40934200-40949400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:40939800-40956800	Strong transcription	Dnd41	blood
32	chr15:40939800-40956800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:40941400-40957600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:40941800-40946800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:40942000-40946400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:40942000-40947400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:40942000-40947600	Strong transcription	HUVEC	blood vessel
38	chr15:40942000-40959000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:40942200-40946000	Weak transcription	Fetal Intestine Large	intestine
40	chr15:40942200-40955800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:40942400-40946400	Strong transcription	NHDF-Ad	bronchial
42	chr15:40942400-40947600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:40942600-40946000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:40942600-40946400	Strong transcription	K562	blood
45	chr15:40942600-40955800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:40942800-40947800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:40943000-40945000	Weak transcription	GM12878-XiMat	blood
48	chr15:40943000-40947400	Weak transcription	Stomach Mucosa	stomach
49	chr15:40943000-40952200	Weak transcription	Fetal Intestine Small	intestine
50	chr15:40943000-40952800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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