Variant report

Variant	rs4607925
Chromosome Location	chr1:171282853-171282854
allele	A/C
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	CREB1	chr1:171282839-171283577	K562	blood:	n/a	n/a
2	TFAP2C	chr1:171282852-171283445	Hela-S3	cervix:	n/a	chr1:171283172-171283187
3	CEBPB	chr1:171282717-171283709	HCT-116	colon:	n/a	chr1:171282864-171282877
4	CTCF	chr1:171282799-171282993	LNCaP	prostate:	n/a	chr1:171282873-171282891 chr1:171282868-171282889
5	CTCF	chr1:171282728-171283302	H1-hESC	embryonic stem cell:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
6	CTCF	chr1:171282791-171283291	Lung_OC	lung:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
7	RAD21	chr1:171282734-171283412	H1-hESC	embryonic stem cell:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
8	REST	chr1:171282816-171283187	Hela-S3	cervix:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
9	RCOR1	chr1:171282853-171283272	GM12878	blood:	n/a	n/a
10	RAD21	chr1:171282655-171283383	H1-hESC	embryonic stem cell:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
11	RAD21	chr1:171282542-171283561	SK-N-SH	brain:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
12	MYC	chr1:171282808-171283547	MCF10A-Er-Src	breast:	n/a	chr1:171283160-171283170
13	RAD21	chr1:171282562-171283551	HCT-116	colon:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
14	TBP	chr1:171282759-171283671	GM12878	blood:	n/a	n/a
15	REST	chr1:171282816-171283231	ECC-1	luminal epithelium:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
16	RAD21	chr1:171282600-171283349	GM12878	blood:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
17	ELF1	chr1:171282809-171283659	HCT-116	colon:	n/a	chr1:171283223-171283236
18	CTCF	chr1:171282813-171283280	LNCaP	prostate:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
19	CTCF	chr1:171282816-171283279	HepG2	liver:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
20	REST	chr1:171282835-171283240	H1-hESC	embryonic stem cell:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
21	REST	chr1:171282700-171283321	PFSK-1	brain:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
22	RAD21	chr1:171282743-171283374	Hela-S3	cervix:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
23	RAD21	chr1:171282842-171283382	ECC-1	luminal epithelium:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
24	SIN3AK20	chr1:171282794-171283552	MCF-7	breast:	n/a	n/a
25	REST	chr1:171282703-171283619	HL-60	blood:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
26	CTCF	chr1:171282758-171283365	IMR90	lung:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
27	CTCF	chr1:171282712-171283360	GM12878	blood:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
28	NRF1	chr1:171282822-171283012	H1-hESC	embryonic stem cell:	n/a	n/a
29	CEBPB	chr1:171282833-171283617	HCT-116	colon:	n/a	chr1:171282864-171282877
30	SMC3	chr1:171282652-171283385	GM12878	blood:	n/a	chr1:171282875-171282889
31	FOXM1	chr1:171282805-171283449	GM12878	blood:	n/a	n/a
32	MAX	chr1:171282599-171283469	NB4	blood:	n/a	chr1:171283160-171283170
33	BHLHE40	chr1:171282485-171283453	GM12878	blood:	n/a	n/a
34	CTCF	chr1:171282825-171283353	Spleen_OC	spleen:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
35	TBL1XR1	chr1:171282597-171283462	GM12878	blood:	n/a	n/a
36	MXI1	chr1:171282847-171283552	GM12878	blood:	n/a	n/a
37	CTCF	chr1:171282720-171282870	HFF	foreskin:	n/a	n/a
38	RAD21	chr1:171282613-171283359	MCF-7	breast:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
39	CTCF	chr1:171282737-171283247	HepG2	liver:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
40	RAD21	chr1:171282757-171283310	SK-N-SH_RA	brain:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
41	ATF2	chr1:171282746-171283366	GM12878	blood:	n/a	n/a
42	SMC3	chr1:171282498-171283454	SK-N-SH	brain:	n/a	chr1:171282875-171282889
43	JUN	chr1:171282712-171283212	H1-hESC	embryonic stem cell:	n/a	chr1:171282913-171282922
44	CTCF	chr1:171282627-171283455	MCF-7	breast:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
45	RAD21	chr1:171282803-171283387	A549	lung:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
46	EP300	chr1:171282569-171283417	GM12878	blood:	n/a	n/a
47	RAD21	chr1:171282703-171283453	H1-hESC	embryonic stem cell:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
48	CTCF	chr1:171282850-171283295	MCF-7	breast:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
49	ELF1	chr1:171282808-171283682	MCF-7	breast:	n/a	chr1:171283223-171283236
50	RUNX3	chr1:171282487-171283311	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:171282676..171283284-chr1:171373985..171374977,4	MCF-7	breast:
2	chr1:170935849..170936463-chr1:171282647..171283201,2	MCF-7	breast:
3	chr1:170936062..170936908-chr1:171282571..171283243,3	MCF-7	breast:

Variant related genes	Relation type
FMO4	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10399602	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10399952	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10798297	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10912672	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10912673	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10912713	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912714	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912723	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126692	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11484641	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11484642	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487396	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12057955	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059179	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12062692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12068552	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070766	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12072043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077231	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077755	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12079141	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080449	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081291	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12091482	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12092985	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12094878	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141555	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12354390	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12726624	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12729885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730181	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742008	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745080	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12747080	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12755975	1.00[JPT][hapmap]
rs12757839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17581251	0.94[ASN][1000 genomes]
rs2006986	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2076322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2284130	1.00[JPT][hapmap]
rs2284131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28741369	1.00[ASN][1000 genomes]
rs34118031	1.00[ASN][1000 genomes]
rs34320519	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55949630	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6424932	0.82[EUR][1000 genomes]
rs6670639	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6674596	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs742350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742351	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512853	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7519999	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7539057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541377	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4607925	FMO4	cis	parietal	SCAN
rs4607925	FMO4	cis	Heart Left Ventricle	GTEx
rs4607925	SELP	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171266600-171288400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:171280000-171283400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr1:171280400-171283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:171280400-171283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:171280800-171283600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:171282400-171283000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:171282400-171283200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr1:171282400-171283400	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:171282400-171284200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:171282600-171283000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:171282600-171283000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:171282600-171283000	Enhancers	Primary B cells from cord blood	blood
13	chr1:171282600-171283000	Enhancers	Liver	Liver
14	chr1:171282600-171283200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:171282600-171283200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:171282600-171283200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:171282600-171283200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:171282600-171283200	Enhancers	Fetal Heart	heart
19	chr1:171282600-171283400	Enhancers	Stomach Mucosa	stomach
20	chr1:171282600-171283600	Active TSS	NHDF-Ad	bronchial
21	chr1:171282600-171283800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:171282600-171284000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:171282600-171284200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:171282800-171283000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:171282800-171283000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr1:171282800-171283000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:171282800-171283000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:171282800-171283000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:171282800-171283000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr1:171282800-171283000	Flanking Active TSS	Osteobl	bone
31	chr1:171282800-171283200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:171282800-171283200	Enhancers	Primary T cells from cord blood	blood
33	chr1:171282800-171283200	Enhancers	Primary hematopoietic stem cells	blood
34	chr1:171282800-171283200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:171282800-171283200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:171282800-171283200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:171282800-171283200	Enhancers	Adipose Nuclei	Adipose
38	chr1:171282800-171283200	Enhancers	Fetal Lung	lung
39	chr1:171282800-171283200	Flanking Active TSS	Dnd41	blood
40	chr1:171282800-171283200	Active TSS	GM12878-XiMat	blood
41	chr1:171282800-171283200	Active TSS	Hela-S3	cervix
42	chr1:171282800-171283200	Enhancers	HUVEC	blood vessel
43	chr1:171282800-171283200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:171282800-171283400	Weak transcription	Fetal Intestine Small	intestine
45	chr1:171282800-171283600	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr1:171282800-171283600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr1:171282800-171283600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:171282800-171283600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:171282800-171283600	Active TSS	Brain Angular Gyrus	brain
50	chr1:171282800-171283600	Active TSS	Brain Anterior Caudate	brain

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