Variant report

Variant	rs56229515
Chromosome Location	chr4:7925093-7925094
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7924008..7927501-chr4:7928282..7930975,3	MCF-7	breast:
2	chr4:7921981..7926079-chr4:7940006..7943093,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11722163	0.92[ASN][1000 genomes]
rs11732100	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733297	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735005	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12509421	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130704	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17177036	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770213	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17770321	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17832709	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28375300	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28417050	0.90[EUR][1000 genomes]
rs28437157	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28438948	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28494514	0.85[EUR][1000 genomes]
rs28544299	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28558196	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28568794	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28600706	0.89[EUR][1000 genomes]
rs28607519	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28622214	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28694545	0.88[EUR][1000 genomes]
rs28766602	0.84[EUR][1000 genomes]
rs34033399	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34310670	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55767717	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844411	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56220381	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56411722	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61742221	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62289320	0.86[EUR][1000 genomes]
rs62289322	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62289333	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62289335	0.90[EUR][1000 genomes]
rs62289336	0.90[EUR][1000 genomes]
rs62289337	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62289338	0.90[EUR][1000 genomes]
rs62289339	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62289340	0.90[EUR][1000 genomes]
rs62289359	0.82[EUR][1000 genomes]
rs62290561	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62290571	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62290573	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62290574	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62290579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813758	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814887	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6815298	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816389	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6829680	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6838073	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6850654	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6855532	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73210862	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73210866	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73214041	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73214042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663026	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7680747	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7687428	0.80[AMR][1000 genomes];0.89[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56229515	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56229515	AFAP1	cis	Whole Blood	GTEx
rs56229515	AFAP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
3	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
4	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
5	chr4:7912800-7931200	Weak transcription	Gastric	stomach
6	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:7913600-7926200	Weak transcription	Fetal Brain Female	brain
11	chr4:7913600-7927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:7913600-7930400	Weak transcription	NHEK	skin
13	chr4:7913800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:7914000-7926800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:7914200-7925800	Weak transcription	HSMMtube	muscle
16	chr4:7914200-7930800	Weak transcription	Fetal Kidney	kidney
17	chr4:7914400-7925600	Weak transcription	HSMM	muscle
18	chr4:7915000-7926000	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:7915000-7928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:7915000-7930400	Weak transcription	Fetal Lung	lung
21	chr4:7918800-7930400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:7919000-7925600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:7919000-7925800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:7919000-7929000	Weak transcription	Brain Germinal Matrix	brain
25	chr4:7919200-7930600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:7919400-7926200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:7919600-7925800	Weak transcription	Fetal Heart	heart
28	chr4:7919600-7930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:7919800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:7919800-7926200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:7919800-7930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:7919800-7931200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:7920000-7925800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:7920000-7925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:7920000-7926000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:7920000-7926400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:7920200-7925800	Weak transcription	NHLF	lung
38	chr4:7920200-7926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:7920400-7926400	Weak transcription	Fetal Intestine Small	intestine
40	chr4:7920400-7926400	Weak transcription	Right Atrium	heart
41	chr4:7920600-7931200	Weak transcription	Lung	lung
42	chr4:7921000-7926400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr4:7921000-7930600	Weak transcription	Esophagus	oesophagus
44	chr4:7921200-7925200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:7921200-7925400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:7921200-7926000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:7921200-7926000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:7921200-7930600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:7921400-7925600	Weak transcription	NH-A	brain
50	chr4:7921600-7925600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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