Variant report

Variant	rs28370977
Chromosome Location	chr4:7894414-7894415
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12641498	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13139805	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13140108	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151529	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1317111	0.90[ASN][1000 genomes]
rs1320070	0.87[ASN][1000 genomes]
rs1320071	0.87[ASN][1000 genomes]
rs1320074	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320075	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435730	0.90[ASN][1000 genomes]
rs17770447	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17833038	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1878325	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385898	0.91[ASN][1000 genomes]
rs2385900	0.89[ASN][1000 genomes]
rs2385901	0.91[ASN][1000 genomes]
rs2385902	0.91[ASN][1000 genomes]
rs2385908	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385909	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2385910	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464089	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28489592	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28631205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28681260	0.83[EUR][1000 genomes]
rs28715921	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28726254	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734123	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28752120	0.83[AMR][1000 genomes]
rs28795989	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2891928	0.92[ASN][1000 genomes]
rs34179701	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34317049	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34505548	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34685551	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34701321	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34984446	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35661042	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4627847	0.90[ASN][1000 genomes]
rs4696746	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696778	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696779	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55937650	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57831033	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811851	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6846317	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848540	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857814	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7437940	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7437984	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7441569	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7655918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686202	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694650	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330348	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938604	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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
rs28370977	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:7881800-7896600	Weak transcription	Lung	lung
4	chr4:7883200-7904400	Weak transcription	Gastric	stomach
5	chr4:7886000-7895800	Weak transcription	Esophagus	oesophagus
6	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
7	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:7891600-7894800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:7891600-7894800	Enhancers	Colon Smooth Muscle	Colon
10	chr4:7891600-7895000	Enhancers	NHDF-Ad	bronchial
11	chr4:7891800-7894800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr4:7891800-7894800	Enhancers	Fetal Heart	heart
13	chr4:7891800-7894800	Enhancers	HMEC	breast
14	chr4:7891800-7895000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr4:7891800-7895400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:7891800-7895800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:7892000-7894600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:7892000-7894600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr4:7892000-7897000	Enhancers	Brain Germinal Matrix	brain
20	chr4:7892400-7894600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:7892400-7894600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr4:7892400-7894600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr4:7892400-7894800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:7892400-7897000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr4:7892600-7894600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:7892600-7894600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:7892600-7894600	Enhancers	Fetal Muscle Leg	muscle
28	chr4:7892600-7894800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:7892600-7903800	Weak transcription	Stomach Mucosa	stomach
30	chr4:7892800-7894600	Enhancers	Fetal Stomach	stomach
31	chr4:7892800-7896000	Enhancers	Fetal Muscle Trunk	muscle
32	chr4:7893000-7894600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:7893000-7902200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:7893200-7894800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:7893200-7895000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:7893200-7895000	Enhancers	HUVEC	blood vessel
37	chr4:7893200-7895000	Enhancers	NHLF	lung
38	chr4:7893200-7896600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:7893200-7903400	Weak transcription	Fetal Kidney	kidney
40	chr4:7893200-7905600	Weak transcription	Brain Angular Gyrus	brain
41	chr4:7893600-7895400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:7893600-7900400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:7893800-7894600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:7893800-7894600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr4:7893800-7894600	Enhancers	Ovary	ovary
46	chr4:7893800-7894600	Enhancers	Right Atrium	heart
47	chr4:7893800-7894800	Flanking Active TSS	NH-A	brain
48	chr4:7893800-7894800	Flanking Active TSS	Osteobl	bone
49	chr4:7893800-7902600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:7894000-7894600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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