Variant report

Variant	rs17476642
Chromosome Location	chr4:15539779-15539780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10017222	1.00[CHB][hapmap]
rs10516289	1.00[CHB][hapmap]
rs11723554	1.00[CHB][hapmap]
rs11729955	1.00[CHB][hapmap]
rs11735063	1.00[CHB][hapmap]
rs16892092	0.85[CEU][hapmap]
rs16892104	0.85[CEU][hapmap]
rs16892107	0.85[CEU][hapmap]
rs17385861	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17385951	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17405797	0.91[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs17405811	1.00[CHB][hapmap]
rs17476879	0.91[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1786	1.00[CHB][hapmap]
rs2302465	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs2302469	0.91[CEU][hapmap]
rs3756247	1.00[CHB][hapmap]
rs3822258	0.91[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4279202	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4301111	1.00[CHB][hapmap]
rs4396986	1.00[CHB][hapmap]
rs4423870	1.00[CHB][hapmap]
rs4549375	1.00[CHB][hapmap]
rs4698390	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4698392	0.81[EUR][1000 genomes]
rs55784324	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56093715	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56094420	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56166932	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6414764	1.00[CHB][hapmap]
rs6815254	1.00[CHB][hapmap]
rs6815296	1.00[CHB][hapmap]
rs6824422	1.00[CHB][hapmap]
rs6826058	1.00[CHB][hapmap]
rs6827406	1.00[CHB][hapmap]
rs6839654	1.00[CHB][hapmap]
rs6848779	1.00[CHB][hapmap]
rs73235013	0.92[ASN][1000 genomes]
rs73235021	0.94[ASN][1000 genomes]
rs73237154	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237171	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73237172	0.81[EUR][1000 genomes]
rs73237182	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73237198	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73239165	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73239167	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73239174	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239175	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239182	0.81[EUR][1000 genomes]
rs73239189	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239191	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73239193	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73241109	0.81[EUR][1000 genomes]
rs73241112	0.81[EUR][1000 genomes]
rs7434484	1.00[CHB][hapmap]
rs767092	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9994518	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17476642	FBXL5	cis	multi-tissue	Pritchard
rs17476642	CD38	cis	cerebellum	SCAN
rs17476642	LOC285550	cis	multi-tissue	Pritchard
rs17476642	FBXL5	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15495600-15559400	Weak transcription	HSMMtube	muscle
3	chr4:15502800-15549200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
5	chr4:15508200-15556400	Weak transcription	Colonic Mucosa	Colon
6	chr4:15508800-15545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:15509200-15564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:15509600-15553400	Weak transcription	HepG2	liver
9	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:15513000-15562400	Weak transcription	Primary B cells from cord blood	blood
11	chr4:15515400-15545200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:15516000-15545600	Weak transcription	Fetal Thymus	thymus
13	chr4:15517800-15551600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
15	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
16	chr4:15520400-15544200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:15520600-15544400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:15520600-15544600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:15520600-15545200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:15520600-15553400	Weak transcription	A549	lung
21	chr4:15520800-15539800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:15520800-15545000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:15522200-15544600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:15526000-15558200	Weak transcription	Spleen	Spleen
25	chr4:15530200-15556600	Weak transcription	HSMM	muscle
26	chr4:15530600-15540000	Weak transcription	NHDF-Ad	bronchial
27	chr4:15530800-15554600	Weak transcription	Placenta	Placenta
28	chr4:15530800-15554600	Weak transcription	NH-A	brain
29	chr4:15531000-15539800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:15531200-15545200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:15531600-15548600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:15533000-15554800	Weak transcription	Fetal Brain Male	brain
33	chr4:15537000-15540400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:15537200-15540200	Strong transcription	Brain Hippocampus Middle	brain
35	chr4:15537200-15565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:15537400-15540400	Strong transcription	Adipose Nuclei	Adipose
37	chr4:15537400-15540400	Strong transcription	Fetal Kidney	kidney
38	chr4:15537400-15540600	Strong transcription	Fetal Stomach	stomach
39	chr4:15537400-15542600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
41	chr4:15537800-15549000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:15538000-15540200	Strong transcription	Liver	Liver
43	chr4:15538000-15540400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:15538000-15540400	Strong transcription	Fetal Lung	lung
45	chr4:15538000-15541000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:15538000-15545800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:15538200-15540200	Strong transcription	NHEK	skin
48	chr4:15538200-15540600	Strong transcription	Brain Germinal Matrix	brain
49	chr4:15538200-15540600	Strong transcription	Ovary	ovary
50	chr4:15538200-15541000	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links