Variant report

Variant	rs3751585
Chromosome Location	chr15:51741056-51741057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10851501	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11070861	0.81[AFR][1000 genomes]
rs11857716	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12324531	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12441057	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12708427	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs12904173	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12904583	1.00[ASN][1000 genomes]
rs1551657	0.86[AFR][1000 genomes]
rs17524750	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17524906	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1902595	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1902596	0.90[CEU][hapmap]
rs2061425	0.90[CEU][hapmap];0.96[AFR][1000 genomes]
rs2252220	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2414112	1.00[YRI][hapmap]
rs2445754	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2446407	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs2459397	1.00[JPT][hapmap]
rs2459399	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs2470167	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2470193	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs28408214	0.81[AFR][1000 genomes]
rs34532503	0.90[AFR][1000 genomes]
rs34662965	0.86[AFR][1000 genomes]
rs34929849	1.00[ASN][1000 genomes]
rs35011964	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4774594	0.81[AFR][1000 genomes]
rs4775954	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap]
rs61618680	0.92[AFR][1000 genomes]
rs6493507	0.81[AFR][1000 genomes]
rs6493511	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6493512	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6493514	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs7180329	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs8026587	0.90[CEU][hapmap]
rs956171	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3751585	SCG3	cis	cerebellum	SCAN
rs3751585	ATP8B4	cis	parietal	SCAN
rs3751585	ARPP19	cis	parietal	SCAN
rs3751585	GATM	cis	cerebellum	SCAN
rs3751585	SCG3	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51734600-51748800	Weak transcription	Fetal Intestine Small	intestine
2	chr15:51735200-51742000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:51735400-51741200	Weak transcription	Brain Germinal Matrix	brain
4	chr15:51735800-51742000	Weak transcription	Fetal Kidney	kidney
5	chr15:51736000-51741200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:51736600-51741400	Weak transcription	Fetal Thymus	thymus
7	chr15:51736800-51751200	Weak transcription	HUVEC	blood vessel
8	chr15:51737000-51775600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr15:51737000-51776400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:51737200-51741600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:51737400-51749000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:51737400-51750200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:51737600-51741600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:51737600-51749200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:51737600-51762400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:51737800-51741200	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:51737800-51748800	Weak transcription	NHDF-Ad	bronchial
18	chr15:51737800-51758400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:51737800-51762400	Weak transcription	Colonic Mucosa	Colon
20	chr15:51738000-51742000	Weak transcription	NH-A	brain
21	chr15:51738000-51755400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr15:51738200-51748800	Weak transcription	Fetal Brain Male	brain
23	chr15:51738200-51784600	Weak transcription	Stomach Mucosa	stomach
24	chr15:51738400-51777400	Weak transcription	Small Intestine	intestine
25	chr15:51738600-51741200	Weak transcription	NHLF	lung
26	chr15:51738600-51742600	Strong transcription	Brain Angular Gyrus	brain
27	chr15:51738600-51742600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:51738600-51743400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr15:51738600-51744600	Strong transcription	Adipose Nuclei	Adipose
30	chr15:51738600-51751800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr15:51738800-51742600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:51738800-51743400	Strong transcription	Placenta	Placenta
33	chr15:51738800-51744600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:51738800-51752000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr15:51738800-51752200	Strong transcription	Fetal Intestine Large	intestine
36	chr15:51738800-51752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:51739000-51742600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:51739000-51749400	Weak transcription	GM12878-XiMat	blood
39	chr15:51739000-51750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:51739000-51752000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:51739000-51752000	Strong transcription	Liver	Liver
42	chr15:51739000-51776000	Weak transcription	Gastric	stomach
43	chr15:51739200-51743000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:51739200-51743000	Strong transcription	HSMMtube	muscle
45	chr15:51739200-51744400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:51739200-51746800	Weak transcription	Right Ventricle	heart
47	chr15:51739200-51748800	Weak transcription	Osteobl	bone
48	chr15:51739400-51741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:51739400-51741200	Weak transcription	Aorta	Aorta
50	chr15:51739400-51741400	Weak transcription	NHEK	skin

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