Variant report

Variant	rs28734123
Chromosome Location	chr4:7888412-7888413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7877407..7880268-chr4:7886566..7889549,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12641498	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13139805	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13140108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151529	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317111	0.87[ASN][1000 genomes]
rs1320070	0.85[ASN][1000 genomes]
rs1320071	0.85[ASN][1000 genomes]
rs1320074	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320075	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13435730	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17770447	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17833038	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1878325	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385898	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2385900	0.86[ASN][1000 genomes]
rs2385901	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2385902	0.89[ASN][1000 genomes]
rs2385908	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385909	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2385910	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28370977	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28464089	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28489592	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28631205	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28681260	0.83[EUR][1000 genomes]
rs28715921	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28726254	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28752120	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28795989	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2891928	0.90[ASN][1000 genomes]
rs34179701	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34317049	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34505548	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34685551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34701321	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34984446	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35661042	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627847	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4696746	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696778	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696779	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55937650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57831033	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62289341	0.81[AFR][1000 genomes]
rs62289351	0.81[AFR][1000 genomes]
rs6811851	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6846317	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848540	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857814	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7437940	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7437984	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7441569	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655918	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7663205	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686202	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7687431	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7694650	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330348	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938604	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28734123	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:72 , 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	chr4:7881800-7889800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:7881800-7896600	Weak transcription	Lung	lung
10	chr4:7883000-7891800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:7883200-7888800	Weak transcription	Placenta	Placenta
12	chr4:7883200-7889400	Weak transcription	Pancreas	Pancrea
13	chr4:7883200-7891800	Weak transcription	Ovary	ovary
14	chr4:7883200-7893000	Weak transcription	Left Ventricle	heart
15	chr4:7883200-7904400	Weak transcription	Gastric	stomach
16	chr4:7884200-7888600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:7884800-7889600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:7884800-7889800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:7884800-7892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:7885000-7890000	Weak transcription	NHEK	skin
21	chr4:7886000-7895800	Weak transcription	Esophagus	oesophagus
22	chr4:7886600-7889000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:7886600-7889000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:7886600-7889800	Enhancers	Rectal Smooth Muscle	rectum
25	chr4:7886600-7890200	Enhancers	Fetal Muscle Leg	muscle
26	chr4:7886800-7889400	Enhancers	Colon Smooth Muscle	Colon
27	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
28	chr4:7887000-7889000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr4:7887000-7889200	Enhancers	NH-A	brain
30	chr4:7887000-7889400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:7887000-7890400	Enhancers	HSMMtube	muscle
32	chr4:7887200-7888800	Enhancers	Brain Germinal Matrix	brain
33	chr4:7887200-7889000	Enhancers	HMEC	breast
34	chr4:7887200-7889200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr4:7887200-7889600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:7887200-7890600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:7887200-7891800	Weak transcription	HepG2	liver
38	chr4:7887400-7888600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:7887400-7889000	Enhancers	Adipose Nuclei	Adipose
40	chr4:7887400-7889400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr4:7887400-7889600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:7887400-7889600	Enhancers	HSMM	muscle
43	chr4:7887400-7890200	Enhancers	Fetal Stomach	stomach
44	chr4:7887600-7889000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr4:7887600-7889200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr4:7887600-7889400	Enhancers	NHLF	lung
47	chr4:7887800-7888600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:7887800-7888600	Active TSS	Aorta	Aorta
49	chr4:7887800-7889200	Flanking Active TSS	Fetal Heart	heart
50	chr4:7887800-7889800	Enhancers	Muscle Satellite Cultured Cells	--

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