Variant report

Variant	rs4073692
Chromosome Location	chr1:171221917-171221918
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	RUNX3	chr1:171221690-171222012	GM12878	blood:	n/a	n/a
2	ATF2	chr1:171221699-171222048	GM12878	blood:	n/a	n/a
3	BHLHE40	chr1:171221707-171222078	GM12878	blood:	n/a	n/a
4	TCF3	chr1:171221557-171222069	GM12878	blood:	n/a	chr1:171221820-171221833 chr1:171221840-171221856
5	TCF12	chr1:171221663-171222025	GM12878	blood:	n/a	n/a
6	TCF3	chr1:171221520-171222086	GM12878	blood:	n/a	chr1:171221820-171221833 chr1:171221840-171221856
7	EP300	chr1:171221694-171222057	GM12878	blood:	n/a	n/a
8	CHD2	chr1:171221750-171222002	GM12878	blood:	n/a	n/a
9	EP300	chr1:171221751-171221987	GM12878	blood:	n/a	n/a
10	IKZF1	chr1:171221817-171222009	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:171221630-171222017	GM12892	blood:	n/a	n/a
12	RUNX3	chr1:171221656-171222054	GM12878	blood:	n/a	n/a
13	ZEB1	chr1:171221647-171222053	GM12878	blood:	n/a	chr1:171221842-171221853
14	TCF12	chr1:171221745-171221982	H1-hESC	embryonic stem cell:	n/a	n/a
15	SPI1	chr1:171221798-171221995	GM12891	blood:	n/a	n/a
16	MAZ	chr1:171221712-171222044	GM12878	blood:	n/a	n/a
17	TCF12	chr1:171221616-171222023	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171219827..171222241-chr1:171222983..171225833,3	MCF-7	breast:

Variant related genes	Relation type
FMO1	TF binding region
ENSG00000231424	TF binding region
ENSG00000206692	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10912616	0.84[ASN][1000 genomes]
rs12065544	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12402732	0.84[ASN][1000 genomes]
rs12403890	0.84[ASN][1000 genomes]
rs12720462	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs16864174	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs16864177	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs16864216	0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1987921	0.84[ASN][1000 genomes]
rs1987944	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2020863	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2049920	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2064077	0.85[ASN][1000 genomes]
rs2072755	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2075988	0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2179106	0.84[ASN][1000 genomes]
rs28369914	0.83[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs3861947	0.82[ASN][1000 genomes]
rs4073693	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4622096	0.98[ASN][1000 genomes]
rs4631734	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4916273	0.83[JPT][hapmap]
rs56370691	0.82[ASN][1000 genomes]
rs57305992	0.84[ASN][1000 genomes]
rs61815363	0.84[ASN][1000 genomes]
rs61815421	0.84[ASN][1000 genomes]
rs61815423	0.84[ASN][1000 genomes]
rs61815424	0.84[ASN][1000 genomes]
rs61815425	0.84[ASN][1000 genomes]
rs61815427	0.84[ASN][1000 genomes]
rs72714167	0.84[ASN][1000 genomes]
rs7533889	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7535210	0.85[ASN][1000 genomes]
rs7551934	0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4073692	FMO2	cis	brain	BrainEAC
rs4073692	FMO2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171222000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:171221000-171222000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr1:171221000-171222000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:171221000-171222000	Bivalent Enhancer	Fetal Thymus	thymus
5	chr1:171221000-171222200	Enhancers	H9 Cell Line	embryonic stem cell
6	chr1:171221000-171222200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr1:171221000-171222600	Enhancers	Dnd41	blood
8	chr1:171221000-171223800	Weak transcription	HMEC	breast
9	chr1:171221000-171224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:171221000-171226000	Weak transcription	Fetal Kidney	kidney
11	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
12	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:171221200-171222000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:171221200-171222000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:171221200-171222000	Enhancers	Fetal Muscle Trunk	muscle
16	chr1:171221200-171222000	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr1:171221200-171222200	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:171221200-171223600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:171221200-171223600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:171221200-171223600	Weak transcription	Osteobl	bone
21	chr1:171221200-171223800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:171221200-171224400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:171221200-171224400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:171221200-171224600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:171221200-171226000	Weak transcription	Liver	Liver
26	chr1:171221200-171226000	Weak transcription	Fetal Lung	lung
27	chr1:171221200-171226400	Weak transcription	Right Atrium	heart
28	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
29	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
30	chr1:171221400-171223800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:171221400-171223800	Weak transcription	NH-A	brain
32	chr1:171221400-171226200	Weak transcription	Fetal Heart	heart
33	chr1:171221600-171222000	Enhancers	Gastric	stomach
34	chr1:171221600-171222000	Enhancers	HSMMtube	muscle
35	chr1:171221800-171222000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:171221800-171222000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:171221800-171222000	Enhancers	Placenta	Placenta
38	chr1:171221800-171222600	Enhancers	GM12878-XiMat	blood
39	chr1:171221800-171222800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:171221800-171223600	Weak transcription	NHEK	skin
41	chr1:171221800-171226400	Weak transcription	Pancreas	Pancrea
42	chr1:171221800-171226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:171221800-171226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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