Variant report

Variant	rs2385909
Chromosome Location	chr4:7905384-7905385
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	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12641498	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13139805	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13140108	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13151529	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1317111	0.86[ASN][1000 genomes]
rs1320070	0.84[ASN][1000 genomes]
rs1320071	0.84[ASN][1000 genomes]
rs1320074	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1320075	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13435730	0.86[ASN][1000 genomes]
rs17770447	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17833038	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1878325	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385898	0.87[ASN][1000 genomes]
rs2385900	0.85[ASN][1000 genomes]
rs2385901	0.87[ASN][1000 genomes]
rs2385902	0.87[ASN][1000 genomes]
rs2385908	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385910	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28370977	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28464089	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28489592	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28631205	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28715921	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28726254	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28734123	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28795989	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2891928	0.89[ASN][1000 genomes]
rs34179701	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34317049	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34505548	0.87[AMR][1000 genomes]
rs34685551	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34701321	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34984446	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35661042	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4627847	0.86[ASN][1000 genomes]
rs4696746	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696778	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696779	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55937650	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57831033	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811851	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846317	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6848540	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857814	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7437940	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7437984	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7441569	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7655918	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7663205	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7686202	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687431	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7694650	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9330348	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs938604	0.91[AMR][1000 genomes];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2385909	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7893200-7905600	Weak transcription	Brain Angular Gyrus	brain
2	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
3	chr4:7894400-7906200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:7895600-7907600	Weak transcription	Colonic Mucosa	Colon
5	chr4:7896800-7907600	Weak transcription	Fetal Intestine Small	intestine
6	chr4:7897000-7907400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:7897400-7905800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:7899200-7905800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:7899600-7907000	Enhancers	Fetal Brain Male	brain
10	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:7900000-7906400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:7900000-7907400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:7900200-7905400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:7900200-7905600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr4:7900200-7912400	Weak transcription	NHEK	skin
16	chr4:7900400-7905800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:7900800-7906000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr4:7901000-7905600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:7901000-7905800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:7901000-7907400	Enhancers	HSMMtube	muscle
22	chr4:7901000-7909000	Enhancers	Fetal Brain Female	brain
23	chr4:7901400-7909400	Enhancers	Fetal Lung	lung
24	chr4:7901600-7905800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:7901600-7907400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
27	chr4:7901800-7905400	Genic enhancers	Osteobl	bone
28	chr4:7901800-7905800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:7901800-7905800	Enhancers	HUVEC	blood vessel
30	chr4:7902000-7909200	Enhancers	Fetal Heart	heart
31	chr4:7902000-7909400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:7902200-7905600	Enhancers	NHDF-Ad	bronchial
33	chr4:7902200-7906200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:7902400-7907600	Enhancers	Rectal Smooth Muscle	rectum
35	chr4:7902600-7905800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:7902600-7906400	Genic enhancers	HSMM	muscle
37	chr4:7903000-7905800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:7903000-7906000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:7903000-7906600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:7903200-7905400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr4:7903200-7906600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:7903200-7907400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:7903400-7905800	Weak transcription	Ovary	ovary
44	chr4:7903400-7911400	Weak transcription	Pancreas	Pancrea
45	chr4:7903400-7911600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:7903600-7915000	Enhancers	Fetal Stomach	stomach
47	chr4:7904000-7905600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr4:7904000-7906800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:7904200-7909400	Enhancers	Right Atrium	heart
50	chr4:7904400-7905400	Enhancers	Lung	lung

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