Variant report

Variant	rs4745571
Chromosome Location	chr9:79318367-79318368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:79318275-79318628	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr9:79318242-79318554	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:79280437..79281078-chr9:79317445..79318438,2	MCF-7	breast:
2	chr9:79277119..79278141-chr9:79318359..79319673,4	MCF-7	breast:
3	chr9:79280496..79281467-chr9:79318110..79319001,3	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000265488	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11145022	0.93[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498266	0.80[JPT][hapmap]
rs511545	0.80[JPT][hapmap]
rs579025	0.80[JPT][hapmap]
rs700757	0.80[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4745571	GCNT1	cis	parietal	SCAN
rs4745571	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79314200-79320000	Enhancers	Fetal Brain Male	brain
3	chr9:79314400-79318800	Enhancers	Fetal Muscle Leg	muscle
4	chr9:79314800-79318800	Enhancers	Fetal Stomach	stomach
5	chr9:79315200-79319400	Weak transcription	Stomach Mucosa	stomach
6	chr9:79315200-79319600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:79315400-79319400	Weak transcription	Fetal Kidney	kidney
9	chr9:79315800-79318400	Weak transcription	Fetal Thymus	thymus
10	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:79316400-79319800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:79316600-79319000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:79316600-79319400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:79316600-79324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:79316800-79319400	Weak transcription	Brain Angular Gyrus	brain
17	chr9:79316800-79319800	Weak transcription	Brain Anterior Caudate	brain
18	chr9:79316800-79322800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:79316800-79325400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:79317200-79319600	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:79317400-79319800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:79317600-79318800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:79317600-79319200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr9:79317600-79319400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:79317600-79319400	Weak transcription	NHDF-Ad	bronchial
30	chr9:79317600-79320000	Weak transcription	Aorta	Aorta
31	chr9:79317600-79330800	Strong transcription	HSMM	muscle
32	chr9:79317800-79318800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:79317800-79328600	Strong transcription	HSMMtube	muscle
34	chr9:79318000-79318400	Active TSS	Primary monocytes fromperipheralblood	blood
35	chr9:79318000-79318400	Active TSS	Primary B cells from cord blood	blood
36	chr9:79318000-79318400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr9:79318000-79318400	Flanking Active TSS	HUVEC	blood vessel
38	chr9:79318000-79318800	Active TSS	Fetal Lung	lung
39	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:79318200-79319000	Strong transcription	Brain Substantia Nigra	brain
41	chr9:79318200-79319400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:79318200-79319400	Weak transcription	Colon Smooth Muscle	Colon

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