Variant report

Variant	rs7680747
Chromosome Location	chr4:7871623-7871624
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	chr4:7870109..7872064-chr4:7879515..7881205,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11732100	0.89[EUR][1000 genomes]
rs11735005	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13130704	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770213	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17770321	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17832709	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375300	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28417050	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437157	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438948	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28494514	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28558196	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28568794	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600706	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622214	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28694545	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28766602	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34033399	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34310670	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55767717	0.80[EUR][1000 genomes]
rs55844411	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56220381	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56229515	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56411722	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61742221	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62289320	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289322	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289333	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289335	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289336	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289337	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289338	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289339	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289340	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289359	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62290561	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290571	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62290573	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290574	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290579	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6813758	0.80[EUR][1000 genomes]
rs6814219	0.85[EUR][1000 genomes]
rs6814887	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815298	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816389	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829680	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838073	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850654	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6855532	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73210862	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73210866	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73214041	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73214042	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7378072	0.84[EUR][1000 genomes]
rs7663026	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687428	0.97[AMR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7680747	AFAP1	cis	Whole Blood	GTEx
rs7680747	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7680747	AFAP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7852600-7873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:7856200-7872800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:7857600-7873000	Weak transcription	Colonic Mucosa	Colon
5	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
6	chr4:7859800-7872600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:7860800-7872800	Weak transcription	Right Ventricle	heart
8	chr4:7861200-7872800	Weak transcription	Psoas Muscle	Psoas
9	chr4:7863800-7872800	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:7864800-7873000	Weak transcription	Primary T cells from cord blood	blood
11	chr4:7865200-7872200	Weak transcription	Right Atrium	heart
12	chr4:7865400-7872600	Weak transcription	Fetal Heart	heart
13	chr4:7865400-7875800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:7865800-7872000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:7865800-7872800	Strong transcription	Fetal Stomach	stomach
16	chr4:7866000-7872000	Weak transcription	Gastric	stomach
17	chr4:7866000-7872600	Weak transcription	Fetal Brain Male	brain
18	chr4:7866000-7872800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:7866000-7872800	Weak transcription	Brain Angular Gyrus	brain
20	chr4:7866000-7872800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:7866000-7872800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:7866000-7872800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:7866000-7872800	Weak transcription	Brain Substantia Nigra	brain
24	chr4:7866000-7873000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:7866000-7873000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:7866000-7873000	Weak transcription	Pancreas	Pancrea
27	chr4:7866000-7874000	Weak transcription	Fetal Kidney	kidney
28	chr4:7866000-7875200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:7866000-7875400	Weak transcription	Stomach Mucosa	stomach
30	chr4:7866000-7877600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:7866000-7877800	Weak transcription	HepG2	liver
32	chr4:7866000-7882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
34	chr4:7866800-7873600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:7867200-7871800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr4:7867200-7872800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:7867200-7873600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:7867400-7873000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:7867400-7873000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:7867400-7873000	Strong transcription	Fetal Intestine Small	intestine
41	chr4:7868400-7872800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr4:7868600-7872800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:7868600-7873400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:7869000-7871800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:7869000-7871800	Genic enhancers	HSMM	muscle
46	chr4:7869000-7872200	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr4:7869000-7873600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:7869200-7872600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:7869200-7880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:7869400-7872800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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