Variant report

Variant	rs61742221
Chromosome Location	chr4:7857230-7857231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11732100	0.87[EUR][1000 genomes]
rs11735005	0.88[EUR][1000 genomes]
rs13130704	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17770213	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17770321	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17832709	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28375300	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28417050	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28437157	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28438948	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28494514	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28544299	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28558196	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28568794	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28600706	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28607519	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28622214	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28694545	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28766602	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34033399	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34310670	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55844411	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56220381	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56229515	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56411722	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62289320	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62289322	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62289333	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62289335	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289336	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289337	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289338	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289339	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289340	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289359	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62290561	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62290571	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62290573	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62290574	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62290579	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6814219	0.85[EUR][1000 genomes]
rs6814887	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6815298	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6816389	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6829680	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6838073	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6850654	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6855532	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73210862	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73210866	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73214041	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73214042	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7378072	0.85[EUR][1000 genomes]
rs7663026	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7680747	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7687428	0.97[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61742221	AFAP1	cis	Whole Blood	GTEx
rs61742221	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs61742221	AFAP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7821200-7859000	Weak transcription	Aorta	Aorta
2	chr4:7830400-7862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:7830600-7862200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:7830600-7862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:7843600-7863000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:7845000-7858600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:7845000-7863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:7845200-7859000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:7846200-7860200	Weak transcription	Small Intestine	intestine
10	chr4:7846800-7858400	Weak transcription	Fetal Heart	heart
11	chr4:7847600-7858400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:7848000-7857400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:7848000-7857400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:7848200-7862000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:7848400-7858200	Weak transcription	Fetal Brain Male	brain
17	chr4:7849400-7857600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:7850000-7857800	Strong transcription	Fetal Intestine Small	intestine
19	chr4:7850400-7857800	Strong transcription	Fetal Intestine Large	intestine
20	chr4:7850400-7858400	Weak transcription	Right Ventricle	heart
21	chr4:7850600-7857400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:7850800-7857400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:7851200-7857400	Strong transcription	NHLF	lung
24	chr4:7851400-7857400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:7851800-7860400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:7852000-7860400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:7852200-7857800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:7852400-7857400	Strong transcription	Ovary	ovary
29	chr4:7852400-7857800	Strong transcription	Fetal Stomach	stomach
30	chr4:7852600-7873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:7853600-7858400	Genic enhancers	NH-A	brain
32	chr4:7853800-7859200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr4:7854000-7858400	Genic enhancers	Fetal Muscle Leg	muscle
34	chr4:7854000-7858600	Genic enhancers	HSMM	muscle
35	chr4:7854000-7859000	Genic enhancers	Osteobl	bone
36	chr4:7854400-7857800	Genic enhancers	Brain Germinal Matrix	brain
37	chr4:7854600-7857600	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr4:7854600-7858400	Weak transcription	Brain Angular Gyrus	brain
39	chr4:7854800-7857800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:7854800-7858400	Weak transcription	Stomach Mucosa	stomach
41	chr4:7855000-7858800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:7855200-7857800	Enhancers	Primary T cells from cord blood	blood
43	chr4:7855200-7857800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:7855200-7857800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr4:7855200-7858000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:7855200-7863400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:7855400-7857400	Strong transcription	Fetal Lung	lung
48	chr4:7855400-7857600	Strong transcription	Lung	lung
49	chr4:7855400-7859400	Strong transcription	NHEK	skin
50	chr4:7855600-7857800	Strong transcription	Rectal Smooth Muscle	rectum

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