Variant report

Variant	rs579025
Chromosome Location	chr9:79305864-79305865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10512061	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11145009	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11145022	0.80[JPT][hapmap]
rs1536820	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2487263	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2553212	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2553213	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4745571	0.80[JPT][hapmap]
rs488165	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs489069	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs498266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506965	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511545	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs519983	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs520365	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs530978	0.83[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs551262	0.83[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs557352	0.83[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs571960	0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs620985	0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap]
rs625426	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630423	0.83[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs641088	0.90[YRI][hapmap]
rs677061	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684639	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs685011	0.83[CEU][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs700757	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs786597	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs579025	TMC1	cis	parietal	SCAN
rs579025	VPS13A	cis	parietal	SCAN
rs579025	PRUNE2	cis	cerebellum	SCAN
rs579025	PRUNE2	cis	Whole Blood	GTEx
rs579025	TLE4	cis	parietal	SCAN
rs579025	KIAA0367	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
2	chr9:79290400-79306000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:79302600-79306600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr9:79302600-79306800	Enhancers	Fetal Intestine Large	intestine
6	chr9:79302600-79306800	Enhancers	Fetal Intestine Small	intestine
7	chr9:79302800-79306600	Weak transcription	Adipose Nuclei	Adipose
8	chr9:79303000-79306600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:79303200-79306000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:79303200-79306000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:79303200-79306200	Enhancers	HepG2	liver
12	chr9:79303400-79306800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:79303600-79306000	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:79303600-79306000	Weak transcription	Gastric	stomach
15	chr9:79303800-79306800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:79304000-79306400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:79304000-79306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:79304200-79306000	Weak transcription	HUVEC	blood vessel
19	chr9:79304200-79306200	Weak transcription	HSMMtube	muscle
20	chr9:79304200-79306400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:79304200-79306600	Weak transcription	Brain Substantia Nigra	brain
22	chr9:79304200-79306600	Weak transcription	NHDF-Ad	bronchial
23	chr9:79304200-79306600	Weak transcription	Osteobl	bone
24	chr9:79304200-79306800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:79304200-79306800	Weak transcription	HMEC	breast
26	chr9:79304200-79307800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:79304400-79306600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:79304400-79306600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:79304600-79306000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr9:79304800-79306600	Enhancers	Duodenum Mucosa	Duodenum
31	chr9:79305000-79306000	Enhancers	Brain Angular Gyrus	brain
32	chr9:79305000-79306000	Weak transcription	Fetal Thymus	thymus
33	chr9:79305000-79306600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr9:79305000-79306600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:79305000-79306800	Enhancers	Fetal Lung	lung
36	chr9:79305000-79307600	Weak transcription	Aorta	Aorta
37	chr9:79305200-79306200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
38	chr9:79305200-79306600	Active TSS	Brain Anterior Caudate	brain
39	chr9:79305200-79306600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr9:79305200-79306800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
41	chr9:79305200-79306800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:79305200-79307200	Enhancers	Colon Smooth Muscle	Colon
43	chr9:79305200-79307600	Enhancers	Stomach Mucosa	stomach
44	chr9:79305400-79306000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr9:79305400-79306400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr9:79305400-79306600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr9:79305400-79306800	Enhancers	Small Intestine	intestine
48	chr9:79305600-79306000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr9:79305600-79306800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr9:79305600-79306800	Genic enhancers	HSMM	muscle

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