Variant report

Variant	rs345502
Chromosome Location	chr4:79221851-79221852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10010118	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10015504	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10023308	0.90[ASN][1000 genomes]
rs10023311	0.90[ASN][1000 genomes]
rs10023496	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10027981	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10028695	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1017649	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs11730296	0.91[ASN][1000 genomes]
rs11736213	0.89[ASN][1000 genomes]
rs12500443	0.80[ASN][1000 genomes]
rs12502886	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12506989	0.81[ASN][1000 genomes]
rs12510741	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12511033	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13117388	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1378239	0.89[ASN][1000 genomes]
rs17455826	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1869646	0.81[MEX][hapmap]
rs1952399	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1958276	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2008786	0.90[ASN][1000 genomes]
rs2168203	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28493765	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2867011	0.81[TSI][hapmap]
rs2867012	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28679752	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34398622	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs345507	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs345529	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35683023	0.89[ASN][1000 genomes]
rs385693	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241623	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859524	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4859918	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4859920	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4859923	0.93[ASN][1000 genomes]
rs4859924	0.93[ASN][1000 genomes]
rs6533565	0.91[ASN][1000 genomes]
rs6533571	0.90[ASN][1000 genomes]
rs6833721	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6854043	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7694740	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7696792	0.90[ASN][1000 genomes]
rs7697230	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9762380	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv818246	chr4:79184338-79221851	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs345502	FBXL17	trans	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79198600-79241400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:79208400-79229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:79208800-79236800	Weak transcription	Fetal Intestine Large	intestine
4	chr4:79214000-79223400	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:79215600-79223000	Weak transcription	Fetal Brain Male	brain
6	chr4:79215600-79229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:79215800-79237600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:79215800-79243800	Weak transcription	Right Ventricle	heart
9	chr4:79217200-79222200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:79217600-79222200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:79218000-79224600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:79218200-79222800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:79218600-79229200	Weak transcription	Fetal Stomach	stomach
14	chr4:79218600-79230000	Weak transcription	Fetal Kidney	kidney
15	chr4:79220000-79228200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:79220200-79222000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:79220200-79223000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr4:79220400-79246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:79220400-79246600	Weak transcription	HMEC	breast
20	chr4:79220600-79222600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:79220600-79229800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:79220600-79234200	Weak transcription	HSMMtube	muscle
23	chr4:79220600-79241400	Weak transcription	Aorta	Aorta
24	chr4:79220800-79222800	Weak transcription	NHLF	lung
25	chr4:79220800-79228600	Weak transcription	Fetal Intestine Small	intestine
26	chr4:79220800-79243000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:79221000-79237400	Weak transcription	Fetal Heart	heart
28	chr4:79221000-79240000	Weak transcription	Psoas Muscle	Psoas
29	chr4:79221200-79228800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:79221200-79229000	Weak transcription	HepG2	liver
31	chr4:79221200-79229200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:79221200-79229800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:79221200-79229800	Weak transcription	Fetal Lung	lung
34	chr4:79221200-79231200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:79221200-79232600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr4:79221200-79263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:79221400-79223000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:79221600-79228200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:79221800-79222600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:79221800-79229000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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