Variant report

Variant	rs17476242
Chromosome Location	chr8:102550842-102550843
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:102532737..102535677-chr8:102549512..102552169,3	MCF-7	breast:
2	chr8:102544008..102547197-chr8:102550488..102554621,4	MCF-7	breast:
3	chr8:102547230..102548755-chr8:102549652..102551659,2	MCF-7	breast:
4	chr8:102550263..102552940-chr8:102564764..102566372,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10505010	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10955256	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10955257	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11776316	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11776725	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11783704	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12114930	0.88[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13256544	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13263539	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13265291	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17397776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880634	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1880635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981361	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2127034	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2127035	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34216075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60028447	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6984360	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs922466	0.92[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024652	chr8:101802121-102587124	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
2	nsv539699	chr8:101802121-102587124	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17476242	FBXO43	cis	cerebellum	SCAN
rs17476242	DCAF13	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102527000-102551200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr8:102527000-102551400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:102527200-102555400	Weak transcription	Fetal Intestine Small	intestine
4	chr8:102527200-102556800	Weak transcription	Fetal Intestine Large	intestine
5	chr8:102533800-102551400	Weak transcription	Pancreas	Pancrea
6	chr8:102546200-102551400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr8:102548400-102551400	Weak transcription	Psoas Muscle	Psoas
8	chr8:102550000-102551600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:102550000-102552200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr8:102550000-102552800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:102550000-102552800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr8:102550000-102553000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr8:102550200-102551000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:102550200-102551000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr8:102550200-102551000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr8:102550200-102551000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:102550200-102551000	Flanking Active TSS	A549	lung
18	chr8:102550200-102551400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:102550200-102551400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr8:102550200-102551400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr8:102550200-102551400	Flanking Active TSS	NHDF-Ad	bronchial
22	chr8:102550200-102551600	Enhancers	Aorta	Aorta
23	chr8:102550200-102551600	Enhancers	Ovary	ovary
24	chr8:102550200-102551600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr8:102550200-102551600	Enhancers	HUVEC	blood vessel
26	chr8:102550200-102551600	Enhancers	NHLF	lung
27	chr8:102550200-102551800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:102550200-102551800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr8:102550200-102551800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr8:102550200-102551800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr8:102550200-102551800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr8:102550200-102551800	Enhancers	Fetal Muscle Leg	muscle
33	chr8:102550200-102551800	Enhancers	NH-A	brain
34	chr8:102550200-102552000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr8:102550200-102552000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr8:102550200-102552000	Enhancers	HMEC	breast
37	chr8:102550200-102552800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr8:102550200-102553000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:102550200-102553200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr8:102550200-102553200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:102550200-102553400	Enhancers	NHEK	skin
42	chr8:102550200-102554000	Enhancers	H9 Cell Line	embryonic stem cell
43	chr8:102550400-102551000	Enhancers	Brain Cingulate Gyrus	brain
44	chr8:102550400-102551200	Enhancers	Brain Hippocampus Middle	brain
45	chr8:102550400-102551400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr8:102550400-102551400	Enhancers	Fetal Lung	lung
47	chr8:102550400-102551400	Enhancers	Fetal Stomach	stomach
48	chr8:102550400-102551600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr8:102550400-102551600	Enhancers	Fetal Heart	heart
50	chr8:102550400-102551600	Enhancers	Fetal Kidney	kidney

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