Variant report

Variant	rs6670639
Chromosome Location	chr1:171226409-171226410
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	MAX	chr1:171226280-171226761	MCF-7	breast:	n/a	chr1:171226442-171226452 chr1:171226496-171226505 chr1:171226496-171226506
2	NFIC	chr1:171226170-171226894	SK-N-SH	brain:	n/a	n/a
3	FOS	chr1:171226223-171226649	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:171226232-171226646	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:171226293-171226557	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr1:171226349-171226636	Hela-S3	cervix:	n/a	chr1:171226442-171226452 chr1:171226496-171226505 chr1:171226496-171226506
7	MXI1	chr1:171226109-171226748	SK-N-SH	brain:	n/a	n/a
8	MYC	chr1:171226132-171226644	MCF10A-Er-Src	breast:	n/a	chr1:171226442-171226452 chr1:171226496-171226505 chr1:171226496-171226506
9	NR2F2	chr1:171226295-171226964	MCF-7	breast:	n/a	n/a
10	CEBPB	chr1:171226221-171226556	HepG2	liver:	n/a	chr1:171226386-171226397
11	CEBPB	chr1:171226110-171226695	MCF-7	breast:	n/a	chr1:171226386-171226397
12	GATA3	chr1:171226234-171226828	MCF-7	breast:	n/a	n/a
13	FOS	chr1:171226239-171226644	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr1:171226251-171226536	A549	lung:	n/a	chr1:171226386-171226397
15	FOS	chr1:171226302-171226657	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr1:171226238-171226645	MCF-7	breast:	n/a	chr1:171226386-171226397
17	CEBPB	chr1:171226327-171226501	K562	blood:	n/a	chr1:171226386-171226397
18	MYC	chr1:171226101-171226673	MCF10A-Er-Src	breast:	n/a	chr1:171226442-171226452 chr1:171226496-171226505 chr1:171226496-171226506
19	NFIC	chr1:171226374-171226865	ECC-1	luminal epithelium:	n/a	n/a
20	STAT3	chr1:171226171-171226549	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr1:171226157-171226560	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA2	chr1:171226094-171226957	SH-SY5Y	brain:	n/a	n/a
23	CEBPB	chr1:171226315-171226515	IMR90	lung:	n/a	chr1:171226386-171226397
24	STAT3	chr1:171226230-171226546	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr1:171226377-171226609	NB4	blood:	n/a	chr1:171226442-171226452 chr1:171226496-171226505 chr1:171226496-171226506
26	CEBPB	chr1:171226215-171226600	Hela-S3	cervix:	n/a	chr1:171226386-171226397
27	E2F4	chr1:171226101-171226561	MCF10A-Er-Src	breast:	n/a	n/a
28	ZNF217	chr1:171226290-171226917	MCF-7	breast:	n/a	n/a
29	NFIC	chr1:171226309-171226955	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
FMO1	TF binding region
ENSG00000206692	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10399602	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10399952	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10798297	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912673	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912713	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10912714	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10912723	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10912736	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1126692	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11484641	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11484642	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11487396	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12057955	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12058402	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12059179	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12062692	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12068552	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12070766	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12072043	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12077231	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12077755	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12079141	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12080449	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12081291	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12091482	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12092985	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12094878	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12141555	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12354390	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12726624	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12729885	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12730181	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12742008	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12745080	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12747080	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12757839	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13376631	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16864302	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16864387	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17581251	0.90[ASN][1000 genomes]
rs2006986	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2076322	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2092311	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2284131	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28741369	0.85[ASN][1000 genomes]
rs34118031	0.85[ASN][1000 genomes]
rs34320519	0.85[ASN][1000 genomes]
rs4607925	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]
rs55949630	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6674596	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs742350	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs742351	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7512853	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7519999	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7539057	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7541377	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6670639	FMO4	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
2	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
4	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
5	chr1:171221800-171226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:171221800-171226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:171222000-171226600	Weak transcription	Placenta	Placenta
8	chr1:171222000-171227200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:171222000-171227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:171224400-171227200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:171224800-171226600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:171224800-171227400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:171224800-171227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:171225000-171227200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:171225000-171227600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:171225000-171228000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:171225600-171227200	Enhancers	Fetal Muscle Leg	muscle
18	chr1:171226000-171226800	Enhancers	Liver	Liver
19	chr1:171226000-171226800	Enhancers	Fetal Kidney	kidney
20	chr1:171226000-171226800	Enhancers	Fetal Lung	lung
21	chr1:171226000-171226800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:171226000-171227200	Enhancers	HMEC	breast
23	chr1:171226000-171227400	Enhancers	Duodenum Mucosa	Duodenum
24	chr1:171226000-171228000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:171226000-171228600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:171226000-171228800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:171226000-171228800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:171226000-171228800	Enhancers	NHEK	skin
29	chr1:171226000-171229200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:171226200-171226600	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:171226200-171226800	Enhancers	Colonic Mucosa	Colon
32	chr1:171226200-171227000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:171226200-171227000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr1:171226200-171227000	Enhancers	Stomach Mucosa	stomach
35	chr1:171226200-171227800	Enhancers	Fetal Heart	heart
36	chr1:171226200-171228800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:171226200-171229200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr1:171226400-171226600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:171226400-171226600	Enhancers	Stomach Smooth Muscle	stomach
40	chr1:171226400-171226800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:171226400-171226800	Enhancers	Gastric	stomach
42	chr1:171226400-171226800	Enhancers	Left Ventricle	heart
43	chr1:171226400-171226800	Enhancers	Psoas Muscle	Psoas
44	chr1:171226400-171226800	Enhancers	Right Atrium	heart
45	chr1:171226400-171226800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr1:171226400-171226800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr1:171226400-171226800	Enhancers	Spleen	Spleen
48	chr1:171226400-171226800	Enhancers	NHDF-Ad	bronchial
49	chr1:171226400-171227000	Enhancers	Fetal Thymus	thymus
50	chr1:171226400-171227000	Enhancers	Pancreas	Pancrea

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