Variant report

Variant	rs1707302
Chromosome Location	chr1:46600917-46600918
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	SMC3	chr1:46600520-46601498	Hela-S3	cervix:	n/a	n/a
2	EP300	chr1:46600280-46601697	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr1:46600466-46601667	ECC-1	luminal epithelium:	n/a	n/a
4	MYC	chr1:46600419-46601571	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr1:46600353-46601460	Hela-S3	cervix:	n/a	chr1:46600577-46600588
6	POLR2A	chr1:46599617-46601123	K562	blood:	n/a	n/a
7	STAT3	chr1:46600473-46601339	MCF10A-Er-Src	breast:	n/a	chr1:46600473-46600484
8	TFAP2C	chr1:46600412-46601492	Hela-S3	cervix:	n/a	chr1:46600834-46600849
9	RCOR1	chr1:46600467-46601003	Hela-S3	cervix:	n/a	n/a
10	EBF1	chr1:46600378-46600942	GM12878	blood:	n/a	chr1:46600664-46600675
11	RAD21	chr1:46600496-46601496	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr1:46600431-46601538	Hela-S3	cervix:	n/a	n/a
13	FOS	chr1:46600426-46601534	MCF10A-Er-Src	breast:	n/a	chr1:46600577-46600588
14	CEBPB	chr1:46600512-46601014	MCF-7	breast:	n/a	chr1:46600679-46600690
15	POLR2A	chr1:46600438-46601030	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr1:46600434-46601345	Hela-S3	cervix:	n/a	chr1:46600473-46600484
17	TBP	chr1:46600467-46601575	Hela-S3	cervix:	n/a	n/a
18	JUN	chr1:46600496-46601452	Hela-S3	cervix:	n/a	chr1:46600577-46600588
19	FOXA1	chr1:46600733-46600983	T-47D	breast:	n/a	n/a
20	TCF12	chr1:46600500-46601040	ECC-1	luminal epithelium:	n/a	n/a
21	EP300	chr1:46600367-46600919	GM12878	blood:	n/a	n/a
22	FOS	chr1:46600359-46601571	MCF10A-Er-Src	breast:	n/a	chr1:46600577-46600588
23	CEBPB	chr1:46600378-46600965	IMR90	lung:	n/a	chr1:46600679-46600690
24	BRCA1	chr1:46600296-46601246	Hela-S3	cervix:	n/a	n/a
25	EP300	chr1:46600637-46601040	T-47D	breast:	n/a	n/a
26	FOS	chr1:46600285-46600924	MCF10A-Er-Src	breast:	n/a	chr1:46600577-46600588
27	SMARCC1	chr1:46600405-46601507	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:46600857-46600921	MCF-7	breast:	n/a	n/a
29	SIN3AK20	chr1:46600379-46601254	MCF-7	breast:	n/a	n/a
30	CEBPB	chr1:46600382-46601605	Hela-S3	cervix:	n/a	chr1:46600679-46600690
31	USF2	chr1:46600433-46601015	Hela-S3	cervix:	n/a	n/a
32	FOS	chr1:46600359-46601501	MCF10A-Er-Src	breast:	n/a	chr1:46600577-46600588
33	GTF2F1	chr1:46600263-46601436	Hela-S3	cervix:	n/a	n/a
34	STAT3	chr1:46600449-46600937	MCF10A-Er-Src	breast:	n/a	chr1:46600473-46600484
35	ESR1	chr1:46600727-46601110	ECC-1	luminal epithelium:	n/a	n/a
36	CHD2	chr1:46600336-46600988	Hela-S3	cervix:	n/a	n/a
37	CEBPB	chr1:46600523-46601052	ECC-1	luminal epithelium:	n/a	chr1:46600679-46600690
38	ESR1	chr1:46600749-46601024	ECC-1	luminal epithelium:	n/a	n/a
39	STAT1	chr1:46600780-46600921	GM12878	blood:	n/a	n/a
40	CEBPB	chr1:46600446-46601105	MCF-7	breast:	n/a	chr1:46600679-46600690
41	WRNIP1	chr1:46600369-46600988	GM12878	blood:	n/a	n/a
42	TFAP2A	chr1:46600486-46601178	Hela-S3	cervix:	n/a	chr1:46600834-46600849
43	STAT3	chr1:46600443-46600978	MCF10A-Er-Src	breast:	n/a	chr1:46600473-46600484
44	EP300	chr1:46600419-46601464	Hela-S3	cervix:	n/a	n/a
45	ESR1	chr1:46600618-46601161	ECC-1	luminal epithelium:	n/a	n/a
46	GATA3	chr1:46600620-46600978	T-47D	breast:	n/a	n/a
47	STAT3	chr1:46600378-46601500	MCF10A-Er-Src	breast:	n/a	chr1:46600473-46600484
48	RFX5	chr1:46600468-46601493	Hela-S3	cervix:	n/a	n/a
49	TCF7L2	chr1:46600544-46600989	Hela-S3	cervix:	n/a	chr1:46600654-46600661
50	MTA3	chr1:46597245-46601010	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46597687..46601092-chr1:46685533..46687921,3	MCF-7	breast:
2	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
3	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
4	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
5	chr1:46595304..46602065-chr1:46660247..46665309,8	MCF-7	breast:
6	chr1:46598477..46601244-chr1:46712967..46714555,2	K562	blood:
7	chr1:46600538..46602719-chr1:109690592..109692888,2	MCF-7	breast:

Variant related genes	Relation type
PIK3R3	TF binding region
ENSG00000117461	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000250719	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10789485	0.95[MEX][hapmap]
rs10789486	0.84[ASW][hapmap];0.90[MEX][hapmap]
rs10890378	0.84[ASW][hapmap];0.90[MEX][hapmap]
rs10890380	0.89[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs10890381	0.80[GIH][hapmap];0.95[MEX][hapmap]
rs11211232	0.95[MEX][hapmap]
rs11211239	0.84[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs11211248	0.84[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs11211257	0.81[ASN][1000 genomes]
rs12090501	0.86[ASN][1000 genomes]
rs1416706	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1473840	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613296	0.88[ASW][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs1622208	0.80[GIH][hapmap];0.95[MEX][hapmap]
rs1707303	0.88[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1707317	0.86[CHB][hapmap]
rs1707322	0.94[ASW][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.88[YRI][hapmap]
rs1707337	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1768801	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1768802	0.88[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap]
rs1768807	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1768809	0.81[MEX][hapmap]
rs1768817	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1768818	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2458400	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2486445	0.89[CHD][hapmap]
rs4073847	0.84[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs4454479	0.84[ASW][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap]
rs4660334	0.84[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs4660341	0.85[ASN][1000 genomes]
rs4660905	0.83[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs6677777	0.84[GIH][hapmap]
rs7538978	0.86[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs785465	0.88[ASW][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap]
rs785467	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs785468	0.88[ASW][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap]
rs785470	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs785480	0.84[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs785483	0.82[ASN][1000 genomes]
rs785484	0.86[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs785486	0.85[ASN][1000 genomes]
rs785490	0.85[ASN][1000 genomes]
rs785493	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs785496	0.85[ASN][1000 genomes]
rs785497	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs785499	0.82[ASN][1000 genomes]
rs785500	0.84[ASN][1000 genomes]
rs785504	0.90[ASN][1000 genomes]
rs785506	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs785510	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs785512	0.88[ASW][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap]
rs785516	0.83[ASN][1000 genomes]
rs785517	0.85[ASN][1000 genomes]
rs785519	0.85[ASN][1000 genomes]
rs796773	0.84[ASN][1000 genomes]
rs925524	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9429095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946524	0.84[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs946527	0.84[ASW][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1707302	CYP4Z1	cis	cerebellum	SCAN
rs1707302	Hs.396207	cis	multi-tissue	Pritchard
rs1707302	NSUN4	cis	cerebellum	SCAN
rs1707302	GPBP1L1	cis	Lymphoblastoid	GTEx
rs1707302	IPP	cis	lymphoblastoid	seeQTL
rs1707302	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs1707302	MAST2	cis	Artery Tibial	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46599200-46601000	Flanking Active TSS	GM12878-XiMat	blood
2	chr1:46599200-46601600	Flanking Active TSS	Hela-S3	cervix
3	chr1:46599200-46603200	Weak transcription	Ovary	ovary
4	chr1:46599400-46601000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:46599400-46601200	Flanking Active TSS	Fetal Heart	heart
6	chr1:46599400-46602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:46599400-46603200	Weak transcription	Liver	Liver
8	chr1:46599600-46601000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:46599600-46601000	Enhancers	Adipose Nuclei	Adipose
10	chr1:46599600-46601000	Enhancers	Fetal Thymus	thymus
11	chr1:46599600-46601000	Enhancers	Psoas Muscle	Psoas
12	chr1:46599600-46601000	Enhancers	A549	lung
13	chr1:46599600-46601200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:46599600-46601200	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr1:46599600-46601200	Enhancers	Fetal Stomach	stomach
16	chr1:46599600-46601400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:46599600-46601400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:46599600-46601600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:46599600-46601600	Enhancers	Fetal Muscle Leg	muscle
20	chr1:46599600-46601600	Enhancers	Left Ventricle	heart
21	chr1:46599600-46603200	Weak transcription	HSMMtube	muscle
22	chr1:46599600-46604000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:46599800-46601000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:46599800-46601000	Enhancers	K562	blood
25	chr1:46599800-46601000	Enhancers	NH-A	brain
26	chr1:46599800-46601000	Enhancers	NHLF	lung
27	chr1:46599800-46601200	Enhancers	HMEC	breast
28	chr1:46599800-46601600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:46599800-46603200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:46600000-46601000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:46600000-46601000	Enhancers	Brain Germinal Matrix	brain
32	chr1:46600000-46601000	Enhancers	Brain Hippocampus Middle	brain
33	chr1:46600000-46601000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr1:46600000-46601400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:46600000-46601600	Enhancers	Fetal Brain Female	brain
36	chr1:46600000-46601800	Enhancers	Fetal Brain Male	brain
37	chr1:46600000-46602400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:46600000-46602400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:46600000-46602600	Weak transcription	Fetal Kidney	kidney
40	chr1:46600000-46603200	Weak transcription	HUVEC	blood vessel
41	chr1:46600000-46604000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:46600200-46601200	Enhancers	NHDF-Ad	bronchial
43	chr1:46600200-46601800	Enhancers	NHEK	skin
44	chr1:46600200-46603200	Weak transcription	Fetal Intestine Large	intestine
45	chr1:46600200-46603200	Weak transcription	Fetal Lung	lung
46	chr1:46600400-46601000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:46600400-46601600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:46600400-46602200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:46600400-46602200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:46600400-46602400	Weak transcription	Aorta	Aorta

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