Variant report

Variant	rs17466832
Chromosome Location	chr4:7752091-7752092
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr4:7752033-7752333	IMR90	lung:	n/a	chr4:7752192-7752207
2	MAFK	chr4:7752023-7752306	HepG2	liver:	n/a	chr4:7752192-7752207
3	FOSL2	chr4:7751222-7752103	A549	lung:	n/a	n/a
4	MAFK	chr4:7752039-7752364	HepG2	liver:	n/a	chr4:7752192-7752207
5	MAFF	chr4:7752013-7752258	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
AFAP1-AS1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13123129	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13151500	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34277472	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34769859	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35384319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv878575	chr4:7715181-7767755	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17466832	CLNK	cis	cerebellum	SCAN
rs17466832	MSX1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7726600-7757200	Weak transcription	Fetal Brain Female	brain
2	chr4:7740200-7765000	Weak transcription	Aorta	Aorta
3	chr4:7740600-7762400	Weak transcription	Pancreas	Pancrea
4	chr4:7741000-7757800	Weak transcription	Lung	lung
5	chr4:7741400-7755000	Weak transcription	Fetal Intestine Small	intestine
6	chr4:7741400-7755200	Weak transcription	Brain Germinal Matrix	brain
7	chr4:7744000-7752800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr4:7746000-7752200	Weak transcription	Esophagus	oesophagus
9	chr4:7746000-7753200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:7746000-7758800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:7746200-7757200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:7746200-7758600	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:7746200-7772000	Weak transcription	Brain Anterior Caudate	brain
14	chr4:7746400-7752400	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr4:7746400-7757800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:7747200-7761800	Weak transcription	Colonic Mucosa	Colon
17	chr4:7748800-7756200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:7749400-7760000	Weak transcription	HSMMtube	muscle
19	chr4:7749400-7765600	Weak transcription	Fetal Brain Male	brain
20	chr4:7749400-7767000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:7749600-7752200	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:7749600-7759000	Weak transcription	Spleen	Spleen
23	chr4:7749800-7757000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:7750600-7752200	Enhancers	Primary T cells from cord blood	blood
25	chr4:7750800-7752400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr4:7750800-7755000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:7751200-7755200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:7751400-7752200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr4:7751400-7752200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr4:7751400-7752400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:7751400-7752400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr4:7751400-7752400	Enhancers	NH-A	brain
33	chr4:7751400-7752600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr4:7751400-7753000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:7751400-7753000	Enhancers	Osteobl	bone
36	chr4:7751400-7753200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:7751400-7753200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:7751400-7754200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:7751400-7758000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr4:7751600-7752600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr4:7751800-7752200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:7751800-7752200	Flanking Active TSS	A549	lung
43	chr4:7751800-7754400	Weak transcription	HMEC	breast
44	chr4:7751800-7754800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:7751800-7761000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:7752000-7752400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:7752000-7753000	Enhancers	Adipose Nuclei	Adipose
48	chr4:7752000-7753000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr4:7752000-7753000	Enhancers	Fetal Stomach	stomach
50	chr4:7752000-7753000	Enhancers	HepG2	liver

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