Variant report

Variant	rs28568794
Chromosome Location	chr4:7852093-7852094
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7804029..7806912-chr4:7851204..7853700,2	MCF-7	breast:
2	chr4:7844578..7847956-chr4:7851101..7853656,4	MCF-7	breast:
3	chr4:7805566..7806506-chr4:7851979..7852511,2	K562	blood:

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

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

rs_ID	r²[population]
rs11732100	0.86[EUR][1000 genomes]
rs11735005	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13130704	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770213	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17770321	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17832709	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375300	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28417050	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437157	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438948	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28494514	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28558196	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28600706	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622214	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28694545	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28766602	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34033399	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34310670	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55844411	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56220381	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56229515	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56411722	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61742221	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62289320	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289322	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289333	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289335	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289336	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289337	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289338	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289339	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289340	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289359	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62290561	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290571	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62290573	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290574	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290579	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6814219	0.84[EUR][1000 genomes]
rs6814887	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815298	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816389	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829680	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838073	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850654	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6855532	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73210862	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73210866	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73214041	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73214042	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7378072	0.84[EUR][1000 genomes]
rs7663026	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680747	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687428	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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
rs28568794	AFAP1	cis	Whole Blood	GTEx
rs28568794	AFAP1	cis	Esophagus Mucosa	GTEx
rs28568794	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7821200-7859000	Weak transcription	Aorta	Aorta
2	chr4:7825600-7852200	Weak transcription	Gastric	stomach
3	chr4:7825800-7854200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:7830400-7862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:7830600-7855200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:7830600-7856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:7830600-7857200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:7830600-7862200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:7830600-7862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:7830800-7854400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:7832200-7854000	Weak transcription	Brain Angular Gyrus	brain
12	chr4:7833800-7855200	Weak transcription	Spleen	Spleen
13	chr4:7836600-7855200	Weak transcription	Fetal Kidney	kidney
14	chr4:7840600-7853400	Weak transcription	Pancreas	Pancrea
15	chr4:7843400-7852400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:7843600-7863000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:7845000-7856400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:7845000-7858600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:7845000-7863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:7845200-7859000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:7846000-7852200	Weak transcription	Colonic Mucosa	Colon
22	chr4:7846200-7853800	Weak transcription	Stomach Mucosa	stomach
23	chr4:7846200-7860200	Weak transcription	Small Intestine	intestine
24	chr4:7846400-7852200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:7846400-7852200	Weak transcription	Placenta	Placenta
26	chr4:7846400-7852200	Weak transcription	Lung	lung
27	chr4:7846400-7853400	Weak transcription	Right Atrium	heart
28	chr4:7846400-7857200	Weak transcription	Left Ventricle	heart
29	chr4:7846600-7852400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:7846600-7853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:7846600-7854200	Weak transcription	Brain Substantia Nigra	brain
32	chr4:7846800-7852200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr4:7846800-7853200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:7846800-7853200	Weak transcription	HepG2	liver
35	chr4:7846800-7858400	Weak transcription	Fetal Heart	heart
36	chr4:7847000-7854000	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:7847200-7854400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:7847600-7858400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:7847800-7853800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:7847800-7854000	Weak transcription	Esophagus	oesophagus
41	chr4:7847800-7855600	Strong transcription	HSMMtube	muscle
42	chr4:7848000-7852400	Weak transcription	HMEC	breast
43	chr4:7848000-7854000	Weak transcription	Brain Anterior Caudate	brain
44	chr4:7848000-7857000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr4:7848000-7857400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:7848000-7857400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr4:7848200-7853600	Strong transcription	NH-A	brain
49	chr4:7848200-7854000	Strong transcription	HSMM	muscle
50	chr4:7848200-7854600	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links