Variant report

Variant	rs6583405
Chromosome Location	chr7:48412335-48412336
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	REST	chr7:48412050-48412489	HL-60	blood:	n/a	chr7:48412280-48412289
2	REST	chr7:48412129-48412404	MCF-7	breast:	n/a	chr7:48412280-48412289

Variant related genes	Relation type
ABCA13	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11972317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11973519	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983883	0.81[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13231603	0.89[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap]
rs1368653	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1433517	0.81[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1433518	0.81[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1433519	0.91[ASN][1000 genomes]
rs1526093	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560792	0.83[JPT][hapmap]
rs1568946	0.82[ASW][hapmap];0.84[JPT][hapmap]
rs17132278	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17132286	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MKK][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17132295	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17172282	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17661752	0.81[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs17661898	0.81[CEU][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17661929	0.81[CEU][hapmap]
rs17712791	0.91[ASN][1000 genomes]
rs1830106	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880739	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117090	0.82[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2117091	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34996049	0.91[ASN][1000 genomes]
rs4145714	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4145715	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4342545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4437599	0.80[CEU][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4917118	0.86[YRI][hapmap]
rs55869793	0.91[ASN][1000 genomes]
rs61532297	0.91[ASN][1000 genomes]
rs62449219	0.80[ASN][1000 genomes]
rs66509041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67631839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946995	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6955132	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6958878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966454	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6974064	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs73097197	0.86[ASN][1000 genomes]
rs73097201	0.90[ASN][1000 genomes]
rs73099309	0.91[ASN][1000 genomes]
rs73099311	0.91[ASN][1000 genomes]
rs73099316	0.91[ASN][1000 genomes]
rs73099324	0.88[ASN][1000 genomes]
rs7780112	0.91[ASN][1000 genomes]
rs7784325	0.81[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7795985	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7803797	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv817336	chr7:48238233-48563988	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1022980	chr7:48243227-48567060	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538833	chr7:48243227-48567060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1022578	chr7:48244414-48584664	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1023575	chr7:48244414-48586685	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1015183	chr7:48244414-48588598	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1032135	chr7:48293104-48414154	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1032221	chr7:48302789-48546684	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv533811	chr7:48313757-48482470	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1015399	chr7:48321542-48544359	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv5733	chr7:48387046-48434029	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
13	esv2761325	chr7:48409639-48557382	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48411000-48427200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:48411400-48413200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:48411600-48414600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr7:48411800-48418600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:48411800-48420400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr7:48412000-48414000	Weak transcription	Primary hematopoietic stem cells	blood

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