Variant report

Variant	rs4073693
Chromosome Location	chr1:171222024-171222025
allele	G/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	ATF2	chr1:171221699-171222048	GM12878	blood:	n/a	n/a
2	BHLHE40	chr1:171221707-171222078	GM12878	blood:	n/a	n/a
3	TCF3	chr1:171221557-171222069	GM12878	blood:	n/a	chr1:171221820-171221833 chr1:171221840-171221856
4	TCF12	chr1:171221663-171222025	GM12878	blood:	n/a	n/a
5	TCF3	chr1:171221520-171222086	GM12878	blood:	n/a	chr1:171221820-171221833 chr1:171221840-171221856
6	EP300	chr1:171221694-171222057	GM12878	blood:	n/a	n/a
7	RUNX3	chr1:171221656-171222054	GM12878	blood:	n/a	n/a
8	ZEB1	chr1:171221647-171222053	GM12878	blood:	n/a	chr1:171221842-171221853
9	MAZ	chr1:171221712-171222044	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
ENSG00000231424	TF binding region
FMO1	TF binding region
ENSG00000206692	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10912616	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12065544	0.81[ASN][1000 genomes]
rs12402732	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12403890	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12720462	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16864174	0.83[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs16864177	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs16864216	0.83[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1987921	0.83[ASN][1000 genomes]
rs1987944	0.83[ASN][1000 genomes]
rs2020863	0.83[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2049920	0.83[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2064077	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2072755	0.83[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2075988	0.83[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs2179106	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28369914	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs3861947	0.81[ASN][1000 genomes]
rs4073692	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4622096	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4631734	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4916273	0.83[JPT][hapmap];0.89[MEX][hapmap]
rs56370691	0.81[ASN][1000 genomes]
rs57305992	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61815363	0.83[ASN][1000 genomes]
rs61815421	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61815423	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61815424	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61815425	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61815427	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72714167	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7533889	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7535210	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7551934	0.82[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171222200	Enhancers	H9 Cell Line	embryonic stem cell
2	chr1:171221000-171222200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
3	chr1:171221000-171222600	Enhancers	Dnd41	blood
4	chr1:171221000-171223800	Weak transcription	HMEC	breast
5	chr1:171221000-171224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:171221000-171226000	Weak transcription	Fetal Kidney	kidney
7	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
8	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:171221200-171222200	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:171221200-171223600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:171221200-171223600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:171221200-171223600	Weak transcription	Osteobl	bone
13	chr1:171221200-171223800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:171221200-171224400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:171221200-171224400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:171221200-171224600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:171221200-171226000	Weak transcription	Liver	Liver
18	chr1:171221200-171226000	Weak transcription	Fetal Lung	lung
19	chr1:171221200-171226400	Weak transcription	Right Atrium	heart
20	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
21	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
22	chr1:171221400-171223800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:171221400-171223800	Weak transcription	NH-A	brain
24	chr1:171221400-171226200	Weak transcription	Fetal Heart	heart
25	chr1:171221800-171222600	Enhancers	GM12878-XiMat	blood
26	chr1:171221800-171222800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:171221800-171223600	Weak transcription	NHEK	skin
28	chr1:171221800-171226400	Weak transcription	Pancreas	Pancrea
29	chr1:171221800-171226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:171221800-171226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:171222000-171223600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:171222000-171223800	Weak transcription	Gastric	stomach
33	chr1:171222000-171224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:171222000-171226200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:171222000-171226400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:171222000-171226600	Weak transcription	Placenta	Placenta
37	chr1:171222000-171227200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:171222000-171227400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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