Variant report

Variant	rs17770213
Chromosome Location	chr4:7896866-7896867
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	chr4:7896306..7899121-chr4:7899762..7902473,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11732100	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11733177	0.86[TSI][hapmap]
rs11733297	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11735005	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11930623	0.89[TSI][hapmap]
rs11945233	0.80[YRI][hapmap]
rs12509421	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs13121514	1.00[JPT][hapmap]
rs13130704	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1320074	0.90[YRI][hapmap]
rs17177036	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17770321	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375300	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28417050	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437157	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28438948	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28494514	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28544299	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28558196	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28568794	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28600706	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28607519	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28622214	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28694545	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28766602	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34033399	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34310670	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55767717	0.81[ASN][1000 genomes]
rs55844411	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56220381	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56229515	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56411722	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61742221	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62289320	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289322	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289333	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289335	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289336	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289337	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289338	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289339	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289340	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289359	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62290561	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290571	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62290573	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62290574	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62290579	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6813758	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6814219	0.82[EUR][1000 genomes]
rs6814887	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6815298	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6816389	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6829680	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6838073	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6850654	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6855532	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73210862	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73210866	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73214041	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73214042	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7378072	0.82[EUR][1000 genomes]
rs7663026	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7680747	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7687428	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17770213	AFAP1	cis	Whole Blood	GTEx
rs17770213	AFAP1	cis	Esophagus Mucosa	GTEx
rs17770213	ABLIM2	cis	cerebellum	SCAN
rs17770213	AFAP	cis	multi-tissue	Pritchard
rs17770213	AFAP1	cis	cerebellum	SCAN
rs17770213	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:7883200-7904400	Weak transcription	Gastric	stomach
3	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
4	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:7892000-7897000	Enhancers	Brain Germinal Matrix	brain
6	chr4:7892400-7897000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr4:7892600-7903800	Weak transcription	Stomach Mucosa	stomach
8	chr4:7893000-7902200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:7893200-7903400	Weak transcription	Fetal Kidney	kidney
10	chr4:7893200-7905600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:7893600-7900400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:7893800-7902600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:7894200-7901000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:7894200-7902000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
16	chr4:7894400-7898200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:7894400-7900400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:7894400-7901000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:7894400-7901000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:7894400-7901400	Weak transcription	Fetal Lung	lung
21	chr4:7894400-7904400	Weak transcription	Left Ventricle	heart
22	chr4:7894400-7906200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:7894600-7898000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:7894600-7898800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:7894600-7898800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:7894600-7899600	Weak transcription	Ovary	ovary
27	chr4:7894600-7900400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:7894600-7901000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:7894600-7902800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:7894800-7899600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:7894800-7900200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:7895000-7898800	Weak transcription	NHDF-Ad	bronchial
33	chr4:7895000-7899000	Weak transcription	NHLF	lung
34	chr4:7895000-7900200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:7895000-7901000	Weak transcription	HSMMtube	muscle
36	chr4:7895000-7901200	Weak transcription	HUVEC	blood vessel
37	chr4:7895200-7899400	Enhancers	Fetal Heart	heart
38	chr4:7895400-7897000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:7895400-7897000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:7895400-7897000	Enhancers	Fetal Thymus	thymus
41	chr4:7895400-7897000	Enhancers	Right Atrium	heart
42	chr4:7895600-7898200	Enhancers	Fetal Brain Female	brain
43	chr4:7895600-7907600	Weak transcription	Colonic Mucosa	Colon
44	chr4:7895800-7897000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:7895800-7897000	Enhancers	Esophagus	oesophagus
46	chr4:7895800-7897000	Flanking Active TSS	HMEC	breast
47	chr4:7895800-7897600	Enhancers	Fetal Brain Male	brain
48	chr4:7896000-7897000	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr4:7896000-7897000	Genic enhancers	Fetal Stomach	stomach
50	chr4:7896000-7897600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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