Variant report

Variant	rs17003109
Chromosome Location	chr4:79217632-79217633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs17003090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17003102	0.87[AMR][1000 genomes]
rs17003104	0.87[AMR][1000 genomes]
rs17003105	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17003106	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17003107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1825417	0.87[AMR][1000 genomes]
rs41391850	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55714031	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55895609	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56323989	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58723665	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59429199	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59522692	0.87[AMR][1000 genomes]
rs61150533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61476761	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812049	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6821829	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6822437	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6834011	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6838026	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6839334	0.87[AMR][1000 genomes]
rs6840763	0.87[AMR][1000 genomes]
rs6855248	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs728200	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827911	0.85[AMR][1000 genomes]
rs73827912	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73827913	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73827916	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827918	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827922	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73827923	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73827934	0.87[AMR][1000 genomes]
rs73827935	0.87[AMR][1000 genomes]
rs73827943	0.87[AMR][1000 genomes]
rs73827946	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73827948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7667557	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7682296	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7687027	0.87[AMR][1000 genomes]
rs7687406	0.87[AMR][1000 genomes]
rs7688218	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7690232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7699637	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs994186	0.87[AMR][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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79188600-79218400	Weak transcription	Aorta	Aorta
2	chr4:79198600-79220200	Weak transcription	Pancreas	Pancrea
3	chr4:79198600-79221000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:79198600-79241400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:79208400-79220800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:79208400-79229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:79208800-79218200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:79208800-79236800	Weak transcription	Fetal Intestine Large	intestine
9	chr4:79210600-79218800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:79212800-79218000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:79213200-79218200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:79213800-79217800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:79214000-79220200	Weak transcription	Fetal Intestine Small	intestine
14	chr4:79214000-79220200	Weak transcription	Psoas Muscle	Psoas
15	chr4:79214000-79223400	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:79215400-79218200	Weak transcription	Brain Germinal Matrix	brain
17	chr4:79215400-79218200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:79215600-79218200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:79215600-79219800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:79215600-79219800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:79215600-79219800	Weak transcription	NHEK	skin
22	chr4:79215600-79220000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:79215600-79220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:79215600-79220200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:79215600-79223000	Weak transcription	Fetal Brain Male	brain
26	chr4:79215600-79229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:79215800-79217800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:79215800-79217800	Weak transcription	HSMMtube	muscle
29	chr4:79215800-79218000	Weak transcription	Hela-S3	cervix
30	chr4:79215800-79218000	Weak transcription	NH-A	brain
31	chr4:79215800-79218000	Weak transcription	NHLF	lung
32	chr4:79215800-79218200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:79215800-79218200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:79215800-79220000	Weak transcription	HMEC	breast
35	chr4:79215800-79237600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:79215800-79243800	Weak transcription	Right Ventricle	heart
37	chr4:79216000-79219000	Weak transcription	HSMM	muscle
38	chr4:79216800-79217800	Weak transcription	Fetal Heart	heart
39	chr4:79217200-79218200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:79217200-79218600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr4:79217200-79218600	Flanking Active TSS	Fetal Lung	lung
42	chr4:79217200-79222200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:79217400-79217800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:79217400-79217800	Weak transcription	Fetal Kidney	kidney
45	chr4:79217400-79217800	Strong transcription	HepG2	liver
46	chr4:79217400-79218000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:79217400-79218200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:79217400-79218200	Enhancers	NHDF-Ad	bronchial
49	chr4:79217400-79218600	Enhancers	Fetal Stomach	stomach
50	chr4:79217400-79218600	Enhancers	Placenta Amnion	Placenta Amnion

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