Variant report

Variant	rs1467742
Chromosome Location	chr1:161050851-161050852
allele	C/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	STAT3	chr1:161050733-161050974	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr1:161050629-161050891	Hela-S3	cervix:	n/a	n/a
3	FOS	chr1:161050672-161050890	MCF10A-Er-Src	breast:	n/a	chr1:161050794-161050801 chr1:161050706-161050718
4	CEBPB	chr1:161050596-161050920	IMR90	lung:	n/a	n/a
5	FOS	chr1:161050597-161051139	MCF10A-Er-Src	breast:	n/a	chr1:161050794-161050801 chr1:161050706-161050718
6	FOS	chr1:161050610-161051015	MCF10A-Er-Src	breast:	n/a	chr1:161050794-161050801 chr1:161050706-161050718
7	MYC	chr1:161050632-161050864	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:161050606-161050935	MCF10A-Er-Src	breast:	n/a	chr1:161050794-161050801 chr1:161050706-161050718

No.	Distal block	Cell Line	Cell type
1	chr1:161020801..161022470-chr1:161048503..161051319,2	K562	blood:
2	chr1:161049380..161051742-chr1:161085768..161089487,3	MCF-7	breast:
3	chr1:161038298..161040861-chr1:161050005..161051745,3	K562	blood:
4	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228917	TF binding region
PVRL4	TF binding region
ENSG00000143256	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000186517	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10908822	0.95[ASN][1000 genomes]
rs11265547	0.95[ASN][1000 genomes]
rs11265549	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142854	0.93[ASN][1000 genomes]
rs12401309	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1556257	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3820097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3892376	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4233364	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656285	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs4656287	0.92[GIH][hapmap]
rs4656288	0.88[GIH][hapmap]
rs4656978	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6671492	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
2	chr1:161039800-161052600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:161039800-161053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:161040200-161052600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:161040200-161052800	Weak transcription	Colonic Mucosa	Colon
6	chr1:161043600-161052800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:161043800-161052200	Weak transcription	Spleen	Spleen
8	chr1:161045000-161052400	Weak transcription	A549	lung
9	chr1:161045000-161053200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:161047400-161053400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:161047600-161052200	Weak transcription	Pancreas	Pancrea
12	chr1:161047600-161053000	Weak transcription	HepG2	liver
13	chr1:161049000-161055000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:161049200-161055600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:161049400-161052800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr1:161049400-161053600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:161049400-161056400	Enhancers	HMEC	breast
18	chr1:161049400-161056600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:161049600-161054600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:161049800-161051600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:161049800-161052800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:161049800-161052800	Enhancers	Placenta	Placenta
23	chr1:161049800-161054600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:161050000-161051200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:161050000-161051200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:161050000-161051200	Enhancers	NH-A	brain
27	chr1:161050000-161051600	Enhancers	HSMMtube	muscle
28	chr1:161050000-161052200	Weak transcription	Gastric	stomach
29	chr1:161050000-161052800	Enhancers	NHEK	skin
30	chr1:161050000-161057800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:161050200-161051000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:161050200-161051000	Active TSS	Esophagus	oesophagus
33	chr1:161050200-161051000	Enhancers	Stomach Mucosa	stomach
34	chr1:161050200-161051200	Enhancers	Osteobl	bone
35	chr1:161050200-161051400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:161050200-161051600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:161050200-161051800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:161050200-161055800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:161050400-161051000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr1:161050400-161051200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:161050400-161051200	Enhancers	NHDF-Ad	bronchial
42	chr1:161050400-161052800	Enhancers	Hela-S3	cervix
43	chr1:161050400-161053600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:161050600-161051000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:161050600-161053600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:161050800-161051000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr1:161050800-161051000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:161050800-161051400	Enhancers	HSMM	muscle
49	chr1:161050800-161051600	Enhancers	Lung	lung
50	chr1:161050800-161052800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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