Variant report

Variant	rs10428666
Chromosome Location	chr5:112673133-112673134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112672794..112674511-chr5:112933592..112935108,2	MCF-7	breast:
2	chr5:112672335..112673213-chr5:112846273..112846906,2	MCF-7	breast:
3	chr5:112672541..112673176-chr5:112942036..112942852,2	K562	blood:

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10077020	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10519343	0.92[EUR][1000 genomes]
rs10519346	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs10900685	0.82[JPT][hapmap]
rs1116547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11241197	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11241201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11241206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11241209	0.86[ASN][1000 genomes]
rs11738075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11738215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11740190	0.92[EUR][1000 genomes]
rs11740233	0.92[EUR][1000 genomes]
rs11740318	0.92[EUR][1000 genomes]
rs11740353	0.92[EUR][1000 genomes]
rs11740443	0.92[EUR][1000 genomes]
rs11741794	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11741916	0.83[ASN][1000 genomes]
rs11741937	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11746532	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11746791	0.92[EUR][1000 genomes]
rs11748058	0.92[EUR][1000 genomes]
rs11748465	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11748503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748524	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11749864	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12152879	0.90[ASN][1000 genomes]
rs12186466	0.89[EUR][1000 genomes]
rs12188069	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs12188070	0.89[EUR][1000 genomes]
rs12188230	0.92[EUR][1000 genomes]
rs12514091	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12516418	0.82[JPT][hapmap]
rs12519753	0.96[ASN][1000 genomes]
rs12520003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12521391	0.84[EUR][1000 genomes]
rs12522683	0.84[EUR][1000 genomes]
rs12522862	0.84[EUR][1000 genomes]
rs12523027	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12523255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12523284	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13360719	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1443683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1517209	0.96[ASN][1000 genomes]
rs1586943	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17135454	0.84[EUR][1000 genomes]
rs17135463	0.84[EUR][1000 genomes]
rs17135506	0.92[EUR][1000 genomes]
rs17135507	0.92[EUR][1000 genomes]
rs17135514	0.92[EUR][1000 genomes]
rs17135515	0.92[EUR][1000 genomes]
rs17135517	0.92[EUR][1000 genomes]
rs17135519	0.92[EUR][1000 genomes]
rs17135520	0.92[EUR][1000 genomes]
rs17135526	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135531	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135546	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17135597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17135608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17135616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17135630	0.82[JPT][hapmap]
rs17164185	0.84[EUR][1000 genomes]
rs1833678	1.00[JPT][hapmap]
rs1838208	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1845289	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1850410	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2042222	0.85[JPT][hapmap]
rs2068923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34271294	0.81[EUR][1000 genomes]
rs3846721	1.00[JPT][hapmap]
rs3846722	0.85[JPT][hapmap]
rs4632792	0.92[EUR][1000 genomes]
rs4705549	0.84[EUR][1000 genomes]
rs4705551	0.85[JPT][hapmap]
rs4705810	0.92[EUR][1000 genomes]
rs4705814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4705817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4705818	0.94[ASN][1000 genomes]
rs4705819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4705826	1.00[JPT][hapmap]
rs56294433	0.81[EUR][1000 genomes]
rs60437559	0.92[EUR][1000 genomes]
rs62374372	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6594695	0.92[EUR][1000 genomes]
rs6594696	0.92[EUR][1000 genomes]
rs6594697	0.92[EUR][1000 genomes]
rs66728961	0.96[ASN][1000 genomes]
rs67303814	0.90[ASN][1000 genomes]
rs67764628	0.92[ASN][1000 genomes]
rs6861786	0.82[ASN][1000 genomes]
rs6864528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6877524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6878001	0.85[JPT][hapmap]
rs6879761	0.84[EUR][1000 genomes]
rs6879800	0.85[JPT][hapmap]
rs6882900	0.82[ASN][1000 genomes]
rs6883441	0.85[JPT][hapmap]
rs73236478	0.94[ASN][1000 genomes]
rs73236479	0.90[ASN][1000 genomes]
rs73244759	0.84[EUR][1000 genomes]
rs73244767	0.89[EUR][1000 genomes]
rs73244770	0.89[EUR][1000 genomes]
rs73244772	0.85[EUR][1000 genomes]
rs73246604	0.92[EUR][1000 genomes]
rs73246629	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73246681	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7703865	0.84[EUR][1000 genomes]
rs7707443	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7717000	0.85[JPT][hapmap]
rs957777	1.00[JPT][hapmap]
rs9800316	0.96[ASN][1000 genomes]

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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112653000-112673600	Weak transcription	Fetal Kidney	kidney
2	chr5:112666800-112678600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:112667000-112674000	Weak transcription	Right Atrium	heart
4	chr5:112667000-112681000	Weak transcription	Esophagus	oesophagus
5	chr5:112667200-112678800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:112667200-112678800	Weak transcription	HMEC	breast
7	chr5:112667200-112680400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:112667200-112680600	Weak transcription	NHEK	skin
9	chr5:112667200-112680800	Weak transcription	Right Ventricle	heart
10	chr5:112667200-112681000	Weak transcription	Pancreas	Pancrea
11	chr5:112667200-112693400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:112671400-112676400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:112672000-112674600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:112672000-112674600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:112672400-112673200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:112672400-112673200	Enhancers	Dnd41	blood
17	chr5:112672400-112674400	Enhancers	NH-A	brain
18	chr5:112672800-112673200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:112672800-112673200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr5:112672800-112673200	Enhancers	Fetal Stomach	stomach
21	chr5:112672800-112673200	Active TSS	Hela-S3	cervix
22	chr5:112672800-112673400	Enhancers	Osteobl	bone
23	chr5:112672800-112673800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:112672800-112675000	Enhancers	Ovary	ovary
25	chr5:112673000-112673200	Bivalent Enhancer	Placenta	Placenta
26	chr5:112673000-112676400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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