Variant report

Variant	rs7557501
Chromosome Location	chr2:63086639-63086640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:63086558-63086757	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000226605	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10153716	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1022110	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11682530	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11688816	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11893131	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713468	0.92[CEU][hapmap]
rs12989754	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs13013218	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs13398408	0.92[YRI][hapmap]
rs13410889	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs13418889	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1420018	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1468748	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1553832	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17027429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1828398	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1877026	0.87[CHD][hapmap]
rs189671	0.92[CEU][hapmap]
rs1906198	0.88[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap]
rs2058566	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2058567	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075375	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs2080227	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2136737	0.92[CEU][hapmap]
rs2215870	0.96[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2421816	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2430388	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2539978	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2539980	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs2539981	0.85[AFR][1000 genomes]
rs2539982	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2539984	0.88[ASN][1000 genomes]
rs2539985	0.91[EUR][1000 genomes]
rs2539987	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2710637	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2710638	0.83[YRI][hapmap]
rs2710639	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2710640	0.94[EUR][1000 genomes]
rs2710642	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs34104251	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs360797	0.93[ASW][hapmap];0.84[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs360799	0.87[CEU][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.91[YRI][hapmap]
rs360800	0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs360801	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs360804	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs360807	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs4461246	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs4671050	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[YRI][hapmap]
rs4671051	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545969	0.83[YRI][hapmap]
rs6545971	1.00[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6545972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545973	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6705798	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6714241	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6739804	0.92[CEU][hapmap];0.87[GIH][hapmap]
rs6757128	0.83[YRI][hapmap]
rs7562149	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7562734	0.87[EUR][1000 genomes]
rs7567923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7571916	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7573756	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[YRI][hapmap]
rs7591708	0.88[CHD][hapmap]
rs9678329	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9789661	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9973612	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[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	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7557501	VPS54	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
2	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
5	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:63054800-63091600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:63061400-63102000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:63062000-63093000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:63071200-63097200	Strong transcription	HepG2	liver
11	chr2:63072600-63101800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:63073400-63093000	Weak transcription	Primary B cells from cord blood	blood
13	chr2:63073800-63091800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:63073800-63094600	Weak transcription	GM12878-XiMat	blood
15	chr2:63074800-63091400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:63074800-63101600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:63075400-63089400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:63075600-63093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:63076400-63101800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:63079000-63092000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:63079000-63101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:63079400-63102000	Weak transcription	HSMMtube	muscle
23	chr2:63079600-63091800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:63079800-63099400	Strong transcription	Liver	Liver
25	chr2:63080000-63088800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:63080600-63092000	Weak transcription	Placenta	Placenta
27	chr2:63080600-63096600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:63081000-63091800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:63081000-63100800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:63081200-63101400	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:63081400-63092000	Weak transcription	NH-A	brain
32	chr2:63081400-63095400	Weak transcription	Psoas Muscle	Psoas
33	chr2:63081400-63101600	Weak transcription	Fetal Brain Male	brain
34	chr2:63081800-63091800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:63082000-63091600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:63082000-63092200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:63082000-63104200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:63082200-63092000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr2:63082400-63102000	Weak transcription	Aorta	Aorta
40	chr2:63082600-63091000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:63082600-63092400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:63082800-63087600	Strong transcription	NHDF-Ad	bronchial
43	chr2:63082800-63101800	Weak transcription	Fetal Thymus	thymus
44	chr2:63082800-63102000	Weak transcription	Thymus	Thymus
45	chr2:63083000-63087200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:63083200-63091200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:63083200-63092600	Weak transcription	NHEK	skin
48	chr2:63083200-63102000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:63083600-63091800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:63083600-63092000	Weak transcription	Brain Germinal Matrix	brain

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