Variant report

Variant	rs17632540
Chromosome Location	chr5:167689296-167689297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:167688954..167689808-chr5:167743024..167744081,6	MCF-7	breast:
2	chr5:167687788..167689812-chr5:167692711..167695181,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113645	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11743857	0.84[AFR][1000 genomes]
rs11743859	0.84[AFR][1000 genomes]
rs12189266	0.81[ASW][hapmap]
rs13164502	0.81[AFR][1000 genomes]
rs17070023	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17070027	1.00[CHB][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs17070030	1.00[ASN][1000 genomes]
rs17070043	1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs17070052	1.00[ASN][1000 genomes]
rs2337158	0.95[LWK][hapmap];0.81[AFR][1000 genomes]
rs55777046	1.00[ASN][1000 genomes]
rs62385560	1.00[ASN][1000 genomes]
rs62385562	1.00[ASN][1000 genomes]
rs62385592	1.00[ASN][1000 genomes]
rs62385593	1.00[ASN][1000 genomes]
rs62385597	1.00[ASN][1000 genomes]
rs62385598	1.00[ASN][1000 genomes]
rs66482664	1.00[ASN][1000 genomes]
rs6868169	0.81[ASW][hapmap];0.95[LWK][hapmap];0.82[AFR][1000 genomes]
rs6868534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6887837	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6888941	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs72835020	1.00[ASN][1000 genomes]
rs73389248	1.00[ASN][1000 genomes]

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	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv5117	chr5:167666701-167711857	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv462512	chr5:167672105-167702041	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv600257	chr5:167672105-167702041	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv527385	chr5:167689296-167691208	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17632540	GABRP	cis	parietal	SCAN
rs17632540	FBLL1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167646800-167695800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:167672200-167695800	Weak transcription	Fetal Heart	heart
3	chr5:167673000-167695600	Weak transcription	Brain Anterior Caudate	brain
4	chr5:167674400-167695800	Weak transcription	Fetal Lung	lung
5	chr5:167674600-167694400	Weak transcription	Fetal Brain Male	brain
6	chr5:167674800-167696000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:167675000-167695800	Weak transcription	Brain Angular Gyrus	brain
8	chr5:167675400-167696000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:167675400-167696000	Weak transcription	Fetal Brain Female	brain
10	chr5:167675800-167696000	Weak transcription	HSMM	muscle
11	chr5:167678800-167696000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:167678800-167696000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:167679000-167696000	Weak transcription	Brain Germinal Matrix	brain
14	chr5:167679200-167695600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:167679600-167694800	Weak transcription	HSMMtube	muscle
16	chr5:167680800-167692000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:167684000-167690400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:167686600-167690800	Strong transcription	NHEK	skin
19	chr5:167686800-167690800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:167687200-167689800	Strong transcription	Right Ventricle	heart
21	chr5:167687200-167692000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:167687400-167689400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr5:167687400-167690000	Strong transcription	Left Ventricle	heart
24	chr5:167687400-167695800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:167688200-167689600	Strong transcription	HMEC	breast
26	chr5:167688400-167696200	Weak transcription	Right Atrium	heart
27	chr5:167688600-167690800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:167688800-167695800	Weak transcription	Liver	Liver
29	chr5:167688800-167695800	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:167689000-167689600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:167689000-167695800	Weak transcription	Fetal Intestine Large	intestine
32	chr5:167689200-167689600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:167689200-167689800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:167689200-167689800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr5:167689200-167689800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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