Variant report

Variant	rs34505548
Chromosome Location	chr4:7889812-7889813
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12641498	0.89[AMR][1000 genomes]
rs13139805	0.89[AMR][1000 genomes]
rs13140108	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13151529	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1320074	0.89[AMR][1000 genomes]
rs1320075	0.90[AMR][1000 genomes]
rs17770447	0.90[AMR][1000 genomes]
rs17833038	0.86[AMR][1000 genomes]
rs1878325	0.90[AMR][1000 genomes]
rs2385908	0.90[AMR][1000 genomes]
rs2385909	0.87[AMR][1000 genomes]
rs2385910	0.90[AMR][1000 genomes]
rs28370977	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28464089	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28489592	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28631205	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28715921	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28726254	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28734123	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28752120	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28795989	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34179701	0.89[AMR][1000 genomes]
rs34317049	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34685551	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34701321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34984446	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35661042	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4696746	0.89[AMR][1000 genomes]
rs4696778	0.86[AMR][1000 genomes]
rs4696779	0.86[AMR][1000 genomes]
rs55937650	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57831033	0.84[AMR][1000 genomes]
rs6811851	0.85[AMR][1000 genomes]
rs6846317	0.84[AMR][1000 genomes]
rs6848540	0.89[AMR][1000 genomes]
rs6857814	0.85[AMR][1000 genomes]
rs7437940	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7437984	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7441569	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7655918	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7663205	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7686202	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7687431	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7694650	0.90[AMR][1000 genomes]
rs9330348	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs938604	0.87[AMR][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	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
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34505548	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
6	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:7879400-7891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:7881800-7896600	Weak transcription	Lung	lung
9	chr4:7883000-7891800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:7883200-7891800	Weak transcription	Ovary	ovary
11	chr4:7883200-7893000	Weak transcription	Left Ventricle	heart
12	chr4:7883200-7904400	Weak transcription	Gastric	stomach
13	chr4:7884800-7892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:7885000-7890000	Weak transcription	NHEK	skin
15	chr4:7886000-7895800	Weak transcription	Esophagus	oesophagus
16	chr4:7886600-7890200	Enhancers	Fetal Muscle Leg	muscle
17	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
18	chr4:7887000-7890400	Enhancers	HSMMtube	muscle
19	chr4:7887200-7890600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:7887200-7891800	Weak transcription	HepG2	liver
21	chr4:7887400-7890200	Enhancers	Fetal Stomach	stomach
22	chr4:7887800-7890200	Enhancers	Fetal Lung	lung
23	chr4:7888200-7893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:7888600-7891800	Weak transcription	Brain Anterior Caudate	brain
25	chr4:7888800-7892000	Weak transcription	Brain Germinal Matrix	brain
26	chr4:7888800-7892400	Weak transcription	Fetal Brain Male	brain
27	chr4:7889000-7890000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:7889000-7890400	Enhancers	Osteobl	bone
29	chr4:7889000-7891800	Weak transcription	Stomach Mucosa	stomach
30	chr4:7889000-7892400	Weak transcription	Adipose Nuclei	Adipose
31	chr4:7889000-7892600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:7889000-7892600	Weak transcription	Aorta	Aorta
33	chr4:7889200-7890000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:7889200-7890000	Weak transcription	NH-A	brain
35	chr4:7889200-7890400	Weak transcription	NHDF-Ad	bronchial
36	chr4:7889200-7892000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:7889200-7892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:7889400-7891800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:7889400-7891800	Weak transcription	HUVEC	blood vessel
41	chr4:7889400-7891800	Weak transcription	NHLF	lung
42	chr4:7889400-7892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:7889600-7890000	Enhancers	Fetal Muscle Trunk	muscle
44	chr4:7889600-7890000	Weak transcription	HSMM	muscle
45	chr4:7889600-7890800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:7889600-7891400	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr4:7889600-7891800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr4:7889600-7892600	Weak transcription	Fetal Kidney	kidney
49	chr4:7889800-7890400	Enhancers	Colon Smooth Muscle	Colon
50	chr4:7889800-7890600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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