Variant report

Variant	rs12507309
Chromosome Location	chr4:69046711-69046712
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	POLR2A	chr4:69046612-69047046	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr4:69046612-69047230	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047
3	STAT3	chr4:69046592-69047230	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047
4	TCF7L2	chr4:69046617-69047183	Hela-S3	cervix:	n/a	n/a
5	FOS	chr4:69046570-69047308	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
6	FOS	chr4:69046573-69047258	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
7	RFX5	chr4:69046601-69046967	Hela-S3	cervix:	n/a	n/a
8	FOS	chr4:69046607-69047219	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
9	POLR2A	chr4:69046473-69047159	MCF10A-Er-Src	breast:	n/a	n/a
10	JUND	chr4:69046571-69047177	Hela-S3	cervix:	n/a	chr4:69047007-69047016
11	E2F4	chr4:69046596-69046811	MCF10A-Er-Src	breast:	n/a	n/a
12	MAZ	chr4:69046655-69046775	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr4:69046607-69047230	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047
14	FOS	chr4:69046652-69047284	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
15	CHD2	chr4:69046647-69047188	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr4:69046666-69047420	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047

Variant related genes	Relation type
FTLP10	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10004522	1.00[CEU][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs10018943	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs10021559	0.83[EUR][1000 genomes]
rs1079449	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs11131735	0.85[EUR][1000 genomes]
rs11131737	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11131739	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11727567	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11731769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11733984	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11940802	0.89[EUR][1000 genomes]
rs11947862	0.90[EUR][1000 genomes]
rs11947869	0.91[EUR][1000 genomes]
rs12501405	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12501540	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12502214	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12502757	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12502946	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503814	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12503983	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12504120	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12504557	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506837	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12507767	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645384	0.89[EUR][1000 genomes]
rs12648112	0.91[EUR][1000 genomes]
rs12651598	0.85[EUR][1000 genomes]
rs13115003	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs13132100	0.91[EUR][1000 genomes]
rs13132990	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13135438	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138038	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs13147736	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13148584	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320264	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13435884	0.89[EUR][1000 genomes]
rs1370828	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1370830	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes]
rs1370832	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1438389	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs1438439	0.91[EUR][1000 genomes]
rs1438440	0.91[EUR][1000 genomes]
rs1438441	0.91[EUR][1000 genomes]
rs1438442	0.91[EUR][1000 genomes]
rs1438443	0.91[EUR][1000 genomes]
rs1438444	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs1438445	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs1438447	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs1530062	0.91[EUR][1000 genomes]
rs1530063	0.95[CEU][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs17089005	0.91[EUR][1000 genomes]
rs17089042	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1837215	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs1866327	0.90[EUR][1000 genomes]
rs1866328	0.91[EUR][1000 genomes]
rs1866329	0.91[EUR][1000 genomes]
rs1898644	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs1946827	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs2118625	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs2164935	1.00[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2319793	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2319798	0.82[ASN][1000 genomes]
rs34237875	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3819257	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4317250	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4374659	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4407557	0.91[EUR][1000 genomes]
rs4538543	0.91[EUR][1000 genomes]
rs4613616	0.91[EUR][1000 genomes]
rs4860273	0.91[CEU][hapmap];0.93[JPT][hapmap]
rs4860274	0.96[CEU][hapmap];0.93[JPT][hapmap]
rs4860275	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs4860276	0.91[EUR][1000 genomes]
rs4860277	0.91[EUR][1000 genomes]
rs4860278	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4860282	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4860897	0.91[EUR][1000 genomes]
rs4860908	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59649794	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6552145	1.00[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66943336	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811052	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs6812743	0.89[EUR][1000 genomes]
rs6819568	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6827417	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6842578	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs71604558	0.92[EUR][1000 genomes]
rs7435855	0.91[EUR][1000 genomes]
rs7674140	0.92[EUR][1000 genomes]
rs939206	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs966827	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs9999589	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1812438	chr4:68943858-69154222	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv4371	chr4:69046637-69081620	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12507309	GCOM2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69046600-69047200	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr4:69046600-69047400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:69046600-69047400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:69046600-69047400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:69046600-69047400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:69046600-69047400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr4:69046600-69047400	Enhancers	HMEC	breast
8	chr4:69046600-69047400	Enhancers	NHEK	skin
9	chr4:69046600-69047800	Enhancers	Hela-S3	cervix

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