Variant report

Variant	rs4724608
Chromosome Location	chr7:47691403-47691404
allele	A/G
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	JUND	chr7:47690982-47691725	SK-N-SH	brain:	n/a	chr7:47691126-47691135
2	GATA3	chr7:47690931-47691693	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr7:47691073-47691513	A549	lung:	n/a	n/a
4	NR3C1	chr7:47690937-47691441	A549	lung:	n/a	n/a
5	PBX3	chr7:47690721-47691819	SK-N-SH	brain:	n/a	chr7:47691127-47691136
6	TEAD4	chr7:47690956-47691662	A549	lung:	n/a	n/a
7	POLR2A	chr7:47690884-47691702	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr7:47690983-47691649	SK-N-SH	brain:	n/a	n/a
9	CEBPB	chr7:47690893-47691705	IMR90	lung:	n/a	chr7:47691352-47691363
10	STAT3	chr7:47690967-47691448	MCF10A-Er-Src	breast:	n/a	chr7:47691371-47691380 chr7:47691370-47691379
11	TCF12	chr7:47690927-47691660	A549	lung:	n/a	chr7:47691215-47691225
12	MAFK	chr7:47691291-47691487	HepG2	liver:	n/a	n/a
13	EP300	chr7:47690777-47691764	A549	lung:	n/a	n/a
14	NR3C1	chr7:47690837-47691605	A549	lung:	n/a	n/a
15	E2F6	chr7:47690732-47691745	A549	lung:	n/a	n/a
16	PBX3	chr7:47690704-47691777	SK-N-SH	brain:	n/a	chr7:47691127-47691136
17	MAFK	chr7:47691236-47691515	HepG2	liver:	n/a	n/a
18	MEF2A	chr7:47690972-47691688	SK-N-SH	brain:	n/a	n/a
19	JUND	chr7:47691178-47691556	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr7:47690824-47691726	IMR90	lung:	n/a	n/a
21	CEBPB	chr7:47690891-47691638	A549	lung:	n/a	chr7:47691352-47691363
22	EP300	chr7:47691078-47691416	SK-N-SH_RA	brain:	n/a	n/a
23	FOXA2	chr7:47690942-47691559	A549	lung:	n/a	n/a
24	GABPA	chr7:47690983-47691565	A549	lung:	n/a	n/a
25	MAFF	chr7:47691244-47691497	HepG2	liver:	n/a	n/a
26	POLR2A	chr7:47691034-47691576	SK-N-SH	brain:	n/a	n/a
27	MAX	chr7:47690924-47691646	SK-N-SH	brain:	n/a	n/a
28	STAT3	chr7:47690968-47691537	MCF10A-Er-Src	breast:	n/a	chr7:47691371-47691380 chr7:47691370-47691379
29	JUND	chr7:47690800-47691659	SK-N-SH	brain:	n/a	chr7:47691126-47691135
30	STAT3	chr7:47690951-47691528	MCF10A-Er-Src	breast:	n/a	chr7:47691371-47691380 chr7:47691370-47691379
31	MYC	chr7:47690953-47691485	MCF10A-Er-Src	breast:	n/a	n/a
32	FOSL2	chr7:47690863-47691747	SK-N-SH	brain:	n/a	chr7:47691126-47691135
33	POLR2A	chr7:47691003-47691629	MCF10A-Er-Src	breast:	n/a	n/a
34	RAD21	chr7:47690761-47691716	A549	lung:	n/a	n/a
35	TCF12	chr7:47690847-47691771	SK-N-SH	brain:	n/a	chr7:47691215-47691225
36	TEAD4	chr7:47690972-47691703	A549	lung:	n/a	n/a
37	SP1	chr7:47690850-47691851	A549	lung:	n/a	chr7:47691115-47691129 chr7:47691117-47691138
38	EP300	chr7:47691091-47691490	Hela-S3	cervix:	n/a	n/a
39	FOSL2	chr7:47690455-47691891	A549	lung:	n/a	chr7:47691126-47691135
40	USF1	chr7:47691037-47691497	A549	lung:	n/a	n/a
41	CEBPB	chr7:47690750-47691715	A549	lung:	n/a	chr7:47691352-47691363
42	GATA3	chr7:47690675-47691910	A549	lung:	n/a	n/a
43	FOXA2	chr7:47691026-47691626	A549	lung:	n/a	n/a
44	CEBPB	chr7:47691027-47691541	Hela-S3	cervix:	n/a	chr7:47691352-47691363
45	MAX	chr7:47690643-47691833	A549	lung:	n/a	n/a
46	GATA3	chr7:47690842-47691604	A549	lung:	n/a	n/a
47	MYC	chr7:47690988-47691494	MCF10A-Er-Src	breast:	n/a	n/a
48	FOSL2	chr7:47691017-47691616	A549	lung:	n/a	chr7:47691126-47691135
49	SIX5	chr7:47691137-47691503	A549	lung:	n/a	n/a
50	ELF1	chr7:47691023-47691562	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:47674185..47676514-chr7:47691065..47692861,2	MCF-7	breast:
2	chr7:47690491..47692702-chr7:47700621..47703207,2	MCF-7	breast:
3	chr7:47679338..47681929-chr7:47689941..47692555,2	MCF-7	breast:

Variant related genes	Relation type
C7orf65	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10951916	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11766347	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs11768009	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11770543	0.80[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12531737	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12535121	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12535169	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12537656	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13242997	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13243511	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35341430	0.82[ASN][1000 genomes]
rs4720603	0.86[ASN][1000 genomes]
rs4724606	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724607	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724609	0.81[CHB][hapmap]
rs4724610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6967317	0.81[ASN][1000 genomes]
rs6968969	0.81[CHB][hapmap]
rs6969715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7790476	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs965924	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4724608	CDC14C	cis	parietal	SCAN
rs4724608	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47687000-47691800	Enhancers	HSMMtube	muscle
2	chr7:47687200-47693200	Weak transcription	Left Ventricle	heart
3	chr7:47687200-47693600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:47687200-47695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:47687400-47692600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:47687400-47693600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:47687600-47693200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:47688000-47693200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:47688000-47693200	Weak transcription	Right Atrium	heart
10	chr7:47688000-47693200	Weak transcription	Spleen	Spleen
11	chr7:47688200-47693400	Weak transcription	Fetal Kidney	kidney
12	chr7:47688800-47692200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:47688800-47693400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr7:47688800-47694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:47689000-47693200	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:47689000-47694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:47689600-47692000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:47689800-47694800	Enhancers	NH-A	brain
19	chr7:47690000-47695000	Enhancers	NHDF-Ad	bronchial
20	chr7:47690200-47693000	Enhancers	HSMM	muscle
21	chr7:47690400-47692600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:47690400-47692600	Enhancers	Aorta	Aorta
23	chr7:47690400-47693200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:47690400-47694800	Enhancers	NHLF	lung
25	chr7:47690600-47691800	Enhancers	Hela-S3	cervix
26	chr7:47690600-47692000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:47690600-47692200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:47690600-47693400	Enhancers	Osteobl	bone
29	chr7:47690600-47695600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:47690800-47691600	Enhancers	Adipose Nuclei	Adipose
31	chr7:47690800-47691600	Enhancers	HMEC	breast
32	chr7:47690800-47691800	Enhancers	Lung	lung
33	chr7:47690800-47691800	Enhancers	NHEK	skin
34	chr7:47690800-47692200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:47690800-47693400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr7:47691000-47691600	Enhancers	HepG2	liver
37	chr7:47691000-47691800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:47691000-47691800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:47691000-47691800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:47691000-47693200	Enhancers	A549	lung
41	chr7:47691000-47693400	Enhancers	Primary B cells from peripheral blood	blood
42	chr7:47691000-47693600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr7:47691200-47693200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr7:47691200-47693200	Weak transcription	Placenta	Placenta
45	chr7:47691400-47691600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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