Variant report

Variant	rs28681260
Chromosome Location	chr4:7896705-7896706
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	chr4:7896306..7899121-chr4:7899762..7902473,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10938695	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13115283	0.86[ASN][1000 genomes]
rs13127935	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13140108	0.83[EUR][1000 genomes]
rs13151529	0.83[EUR][1000 genomes]
rs16841407	0.80[AMR][1000 genomes]
rs28370977	0.83[EUR][1000 genomes]
rs28464089	0.83[EUR][1000 genomes]
rs28500712	0.89[ASN][1000 genomes]
rs28631205	0.80[EUR][1000 genomes]
rs28715921	0.82[EUR][1000 genomes]
rs28734123	0.83[EUR][1000 genomes]
rs34685551	0.83[EUR][1000 genomes]
rs34984446	0.82[EUR][1000 genomes]
rs35661042	0.83[EUR][1000 genomes]
rs4549363	0.86[ASN][1000 genomes]
rs55937650	0.83[EUR][1000 genomes]
rs59521811	0.82[ASN][1000 genomes]
rs6824410	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6831381	0.84[ASN][1000 genomes]
rs6839119	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6844956	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6845653	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7437940	0.82[EUR][1000 genomes]
rs7437984	0.83[EUR][1000 genomes]
rs7441569	0.83[EUR][1000 genomes]
rs7655918	0.83[EUR][1000 genomes]
rs7663205	0.83[EUR][1000 genomes]
rs7687431	0.84[EUR][1000 genomes]
rs9330348	0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28681260	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:7883200-7904400	Weak transcription	Gastric	stomach
3	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
4	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:7892000-7897000	Enhancers	Brain Germinal Matrix	brain
6	chr4:7892400-7897000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr4:7892600-7903800	Weak transcription	Stomach Mucosa	stomach
8	chr4:7893000-7902200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:7893200-7903400	Weak transcription	Fetal Kidney	kidney
10	chr4:7893200-7905600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:7893600-7900400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:7893800-7902600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:7894200-7901000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:7894200-7902000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
16	chr4:7894400-7898200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:7894400-7900400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:7894400-7901000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:7894400-7901000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:7894400-7901400	Weak transcription	Fetal Lung	lung
21	chr4:7894400-7904400	Weak transcription	Left Ventricle	heart
22	chr4:7894400-7906200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:7894600-7896800	Genic enhancers	HSMM	muscle
24	chr4:7894600-7898000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:7894600-7898800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:7894600-7898800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:7894600-7899600	Weak transcription	Ovary	ovary
28	chr4:7894600-7900400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:7894600-7901000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:7894600-7902800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:7894800-7899600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:7894800-7900200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:7895000-7898800	Weak transcription	NHDF-Ad	bronchial
34	chr4:7895000-7899000	Weak transcription	NHLF	lung
35	chr4:7895000-7900200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:7895000-7901000	Weak transcription	HSMMtube	muscle
37	chr4:7895000-7901200	Weak transcription	HUVEC	blood vessel
38	chr4:7895200-7896800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:7895200-7899400	Enhancers	Fetal Heart	heart
40	chr4:7895400-7896800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:7895400-7896800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr4:7895400-7896800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:7895400-7897000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:7895400-7897000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:7895400-7897000	Enhancers	Fetal Thymus	thymus
46	chr4:7895400-7897000	Enhancers	Right Atrium	heart
47	chr4:7895600-7896800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr4:7895600-7896800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr4:7895600-7896800	Strong transcription	Fetal Intestine Small	intestine
50	chr4:7895600-7898200	Enhancers	Fetal Brain Female	brain

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