Variant report

Variant	rs13242531
Chromosome Location	chr7:3688114-3688115
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	MYC	chr7:3688008-3688207	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr7:3687965-3688314	MCF10A-Er-Src	breast:	n/a	chr7:3688146-3688154 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155
3	FOS	chr7:3688022-3688304	MCF10A-Er-Src	breast:	n/a	chr7:3688146-3688154 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155
4	FOS	chr7:3687963-3688331	MCF10A-Er-Src	breast:	n/a	chr7:3688146-3688154 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155
5	STAT3	chr7:3687845-3688306	MCF10A-Er-Src	breast:	n/a	chr7:3688030-3688039 chr7:3688029-3688038 chr7:3688024-3688044 chr7:3688027-3688041
6	STAT3	chr7:3687929-3688304	MCF10A-Er-Src	breast:	n/a	chr7:3688030-3688039 chr7:3688029-3688038 chr7:3688024-3688044 chr7:3688027-3688041
7	E2F4	chr7:3688001-3688395	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr7:3687872-3688281	MCF10A-Er-Src	breast:	n/a	chr7:3688030-3688039 chr7:3688029-3688038 chr7:3688024-3688044 chr7:3688027-3688041
9	FOS	chr7:3687949-3688323	MCF10A-Er-Src	breast:	n/a	chr7:3688146-3688154 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155 chr7:3688145-3688155

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3522949..3523470-chr7:3687761..3688597,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236510	TF binding region

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10226719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10228744	0.85[JPT][hapmap]
rs10245071	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10250929	1.00[JPT][hapmap]
rs10257937	0.88[ASN][1000 genomes]
rs10264803	1.00[JPT][hapmap]
rs10274012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10485876	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951207	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10951255	0.90[MEX][hapmap];0.85[YRI][hapmap]
rs10951265	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10951266	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951272	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951273	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763915	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11765058	0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs11766767	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768609	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs11769660	0.81[ASN][1000 genomes]
rs11770829	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771990	1.00[ASN][1000 genomes]
rs11773388	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12531560	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531698	0.82[YRI][hapmap]
rs12533563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534865	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12535021	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12535467	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12536371	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12536753	0.85[ASN][1000 genomes]
rs12537980	1.00[ASN][1000 genomes]
rs12538202	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539289	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs12540148	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12540209	0.94[ASN][1000 genomes]
rs12701005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs12701014	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13223065	0.82[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs13223852	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13239833	0.88[ASN][1000 genomes]
rs13240060	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240393	0.97[ASN][1000 genomes]
rs13247619	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1522502	0.85[YRI][hapmap]
rs17256676	0.89[TSI][hapmap]
rs17320730	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1922016	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2002669	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2033441	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2082360	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099302	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341579	0.85[ASN][1000 genomes]
rs2341580	0.85[ASN][1000 genomes]
rs2341584	0.82[JPT][hapmap]
rs2341585	0.82[ASN][1000 genomes]
rs2341586	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2614950	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2614951	0.91[ASN][1000 genomes]
rs2614955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2614957	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2705604	0.82[ASN][1000 genomes]
rs2705609	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2880085	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2880087	1.00[JPT][hapmap]
rs34024103	0.82[ASN][1000 genomes]
rs34108699	0.88[ASN][1000 genomes]
rs34188874	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263851	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34369020	1.00[ASN][1000 genomes]
rs34703718	0.97[ASN][1000 genomes]
rs34704704	0.82[ASN][1000 genomes]
rs34784806	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34872052	0.82[ASN][1000 genomes]
rs34953429	0.82[ASN][1000 genomes]
rs35453716	0.82[ASN][1000 genomes]
rs35513976	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35635220	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35669868	0.82[ASN][1000 genomes]
rs36005986	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3919653	0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4342491	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4719998	1.00[ASN][1000 genomes]
rs4719999	1.00[ASN][1000 genomes]
rs4720001	0.97[ASN][1000 genomes]
rs4722903	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4722976	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4722993	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722994	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4722995	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722997	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723001	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4723014	0.86[MEX][hapmap]
rs62437874	0.82[ASN][1000 genomes]
rs62437895	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437901	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440182	0.82[ASN][1000 genomes]
rs6462216	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67062941	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956079	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974350	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974872	0.94[ASN][1000 genomes]
rs71527450	0.89[ASN][1000 genomes]
rs73037689	0.82[ASN][1000 genomes]
rs752587	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs7779391	1.00[JPT][hapmap]
rs956393	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648355	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs968775	0.82[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv948390	chr7:3609821-3734421	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1033415	chr7:3616095-3753563	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv538680	chr7:3616095-3753563	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1016930	chr7:3627295-3705057	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv530553	chr7:3629504-3736851	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1016270	chr7:3650882-3753563	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv538681	chr7:3650882-3753563	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv605934	chr7:3687012-3738147	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13242531	SDK1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3671000-3695600	Weak transcription	Fetal Intestine Small	intestine
2	chr7:3676200-3688600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:3679800-3690400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr7:3681200-3695400	Weak transcription	Spleen	Spleen
5	chr7:3683000-3693000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:3683200-3695600	Weak transcription	Pancreas	Pancrea
7	chr7:3683400-3688400	Weak transcription	Aorta	Aorta
8	chr7:3683400-3693400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:3683800-3696000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:3687800-3688200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:3687800-3688200	Enhancers	NHDF-Ad	bronchial
12	chr7:3687800-3688400	Enhancers	Muscle Satellite Cultured Cells	--

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