Variant report

Variant	rs1337387
Chromosome Location	chr9:16628401-16628402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1003069	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10810578	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10810580	0.81[CEU][hapmap]
rs10810581	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10810583	0.84[AFR][1000 genomes]
rs1337389	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1337390	0.83[CEU][hapmap];0.95[CHB][hapmap];0.88[EUR][1000 genomes]
rs2050617	0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs4112791	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4961727	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7034582	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7039706	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9886876	0.95[CHB][hapmap]

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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1337387	SLC24A2	cis	parietal	SCAN
rs1337387	SEC23A	trans	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16622400-16628600	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr9:16622400-16628600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr9:16622400-16628800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:16622600-16628600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr9:16624200-16629000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:16624200-16629200	Enhancers	Fetal Stomach	stomach
7	chr9:16624200-16630400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:16624400-16628800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr9:16624600-16628800	Enhancers	Fetal Kidney	kidney
10	chr9:16624800-16628600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr9:16624800-16628800	Enhancers	Fetal Thymus	thymus
12	chr9:16625000-16630000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:16625600-16629000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:16625800-16629600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:16625800-16629600	Enhancers	Fetal Muscle Leg	muscle
16	chr9:16626600-16628600	Enhancers	Adipose Nuclei	Adipose
17	chr9:16626600-16628800	Enhancers	Brain Germinal Matrix	brain
18	chr9:16627000-16628600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr9:16627000-16628600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:16627000-16629600	Enhancers	NH-A	brain
21	chr9:16627000-16636600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:16627200-16628800	Enhancers	A549	lung
23	chr9:16627200-16631800	Weak transcription	NHEK	skin
24	chr9:16627200-16637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:16627400-16628600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:16627400-16629200	Enhancers	Colon Smooth Muscle	Colon
27	chr9:16627800-16628600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:16627800-16628800	Flanking Active TSS	HUVEC	blood vessel
29	chr9:16627800-16628800	Flanking Active TSS	Osteobl	bone
30	chr9:16628000-16628800	Flanking Active TSS	Fetal Lung	lung
31	chr9:16628000-16629000	Flanking Active TSS	HSMMtube	muscle
32	chr9:16628200-16628600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:16628200-16628600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:16628200-16628600	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr9:16628200-16628800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:16628200-16628800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:16628200-16628800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:16628200-16628800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:16628200-16628800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:16628200-16628800	Active TSS	Ovary	ovary
41	chr9:16628200-16628800	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr9:16628200-16628800	Flanking Active TSS	HSMM	muscle
43	chr9:16628200-16628800	Flanking Active TSS	NHDF-Ad	bronchial
44	chr9:16628400-16628600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:16628400-16628600	Enhancers	Placenta	Placenta
46	chr9:16628400-16628600	Enhancers	Right Atrium	heart
47	chr9:16628400-16628800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:16628400-16628800	Enhancers	Small Intestine	intestine
49	chr9:16628400-16628800	Flanking Active TSS	Dnd41	blood
50	chr9:16628400-16629200	Flanking Active TSS	NHLF	lung

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