Variant report

Variant	rs12649477
Chromosome Location	chr4:8280066-8280067
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8276758..8278622-chr4:8279545..8282150,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12642594	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28666773	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4280715	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4438745	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4438746	0.89[EUR][1000 genomes]
rs4535324	0.81[AMR][1000 genomes]
rs6447854	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7665567	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv878594	chr4:8154534-8286916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv878599	chr4:8195705-8293398	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv593627	chr4:8202211-8311043	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv878600	chr4:8209447-8312158	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	nsv461218	chr4:8254784-8320126	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
14	nsv593628	chr4:8254784-8320126	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12649477	AFAP1,LOC389199	cis	occipital cortex	BrainEAC

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8272600-8282200	Enhancers	Primary hematopoietic stem cells	blood
2	chr4:8272800-8283400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:8273400-8284000	Enhancers	Fetal Muscle Leg	muscle
4	chr4:8273800-8283800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:8273800-8287400	Enhancers	Fetal Heart	heart
6	chr4:8274200-8281800	Enhancers	Placenta	Placenta
7	chr4:8274600-8281200	Enhancers	Colon Smooth Muscle	Colon
8	chr4:8274800-8281400	Enhancers	Ovary	ovary
9	chr4:8275000-8280200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:8275000-8280600	Enhancers	Rectal Smooth Muscle	rectum
11	chr4:8275200-8281200	Enhancers	Adipose Nuclei	Adipose
12	chr4:8275600-8283800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:8275800-8281600	Enhancers	NHDF-Ad	bronchial
14	chr4:8276000-8280400	Enhancers	Left Ventricle	heart
15	chr4:8276000-8281200	Enhancers	Fetal Lung	lung
16	chr4:8276000-8281400	Enhancers	NHLF	lung
17	chr4:8276200-8280800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:8276200-8281600	Enhancers	HSMM	muscle
19	chr4:8276400-8283800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:8276400-8284400	Weak transcription	Spleen	Spleen
21	chr4:8276800-8281800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:8277200-8280200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:8277200-8281600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:8277600-8280600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:8277800-8281200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:8277800-8281400	Enhancers	Osteobl	bone
27	chr4:8278000-8281600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:8278400-8280800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr4:8278400-8281400	Enhancers	A549	lung
30	chr4:8278400-8281400	Enhancers	NH-A	brain
31	chr4:8278600-8280200	Enhancers	Colonic Mucosa	Colon
32	chr4:8278600-8280600	Enhancers	Duodenum Mucosa	Duodenum
33	chr4:8278600-8283200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:8278800-8280200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr4:8279000-8280800	Enhancers	Fetal Intestine Small	intestine
36	chr4:8279000-8317200	Weak transcription	Gastric	stomach
37	chr4:8279200-8281400	Enhancers	Fetal Stomach	stomach
38	chr4:8279400-8280200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:8279400-8280600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:8279400-8280600	Enhancers	Fetal Intestine Large	intestine
41	chr4:8279400-8281000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr4:8279400-8281400	Enhancers	HSMMtube	muscle
43	chr4:8279600-8280600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:8279600-8280600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr4:8279600-8280600	Enhancers	HUVEC	blood vessel
46	chr4:8279600-8280800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr4:8279600-8281400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:8279600-8281800	Weak transcription	Lung	lung
49	chr4:8279800-8280600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:8279800-8280600	Enhancers	HMEC	breast

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