Variant report

Variant	rs56078222
Chromosome Location	chr4:7932073-7932074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7930429..7933293-chr4:7935968..7937557,2	MCF-7	breast:
2	chr4:7930761..7932557-chr4:7940188..7942388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11733177	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930623	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17771470	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55938116	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62290601	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73214051	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3388730	chr4:7932073-7932121	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56078222	AFAP1	cis	Esophagus Mucosa	GTEx
rs56078222	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56078222	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
2	chr4:7926600-7936600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:7926800-7935400	Weak transcription	Fetal Brain Male	brain
4	chr4:7927800-7932400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:7928200-7932200	Enhancers	Colon Smooth Muscle	Colon
6	chr4:7930400-7932200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:7930400-7932200	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr4:7930400-7932400	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr4:7930400-7934000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:7930600-7932200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr4:7930600-7932200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr4:7930600-7932200	Enhancers	Colonic Mucosa	Colon
13	chr4:7930600-7932200	Enhancers	Fetal Muscle Leg	muscle
14	chr4:7930600-7932200	Enhancers	Pancreas	Pancrea
15	chr4:7930600-7932200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr4:7930600-7932200	Enhancers	HSMM	muscle
17	chr4:7930600-7932400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:7930600-7932400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr4:7930600-7932400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:7930600-7932400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:7930600-7932400	Enhancers	Esophagus	oesophagus
22	chr4:7930600-7932600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:7930600-7932600	Enhancers	Placenta	Placenta
24	chr4:7930600-7935600	Genic enhancers	Osteobl	bone
25	chr4:7930800-7932200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr4:7930800-7932400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:7930800-7932400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:7930800-7932400	Enhancers	HMEC	breast
29	chr4:7931000-7932200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr4:7931000-7932200	Flanking Active TSS	Hela-S3	cervix
31	chr4:7931000-7932400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:7931000-7932800	Enhancers	HUVEC	blood vessel
33	chr4:7931000-7933000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:7931000-7933000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:7931200-7932200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:7931200-7932200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:7931200-7932200	Enhancers	Right Atrium	heart
38	chr4:7931200-7932200	Flanking Active TSS	A549	lung
39	chr4:7931200-7932400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:7931200-7932400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:7931200-7933000	Enhancers	Fetal Heart	heart
42	chr4:7931400-7932200	Enhancers	Fetal Intestine Small	intestine
43	chr4:7931400-7932200	Enhancers	NH-A	brain
44	chr4:7931400-7932400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:7931400-7935400	Weak transcription	Fetal Brain Female	brain
46	chr4:7931400-7939800	Weak transcription	Fetal Kidney	kidney
47	chr4:7931600-7932600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:7931600-7934400	Weak transcription	Fetal Intestine Large	intestine
49	chr4:7931600-7939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:7931600-7939600	Weak transcription	Ovary	ovary

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