Variant report

Variant	rs17135519
Chromosome Location	chr5:112602562-112602563
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112597661..112600348-chr5:112601306..112603277,2	MCF-7	breast:
2	chr5:112543815..112546269-chr5:112600639..112603401,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10428666	0.92[EUR][1000 genomes]
rs10519343	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519346	0.82[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11241197	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740045	0.82[AMR][1000 genomes]
rs11740190	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740233	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740318	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740353	1.00[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11740443	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11741794	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11741937	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11743052	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11744606	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11746532	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11746791	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11746821	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11748058	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11748465	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11748503	0.92[EUR][1000 genomes]
rs11748524	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11749864	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12186466	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12188069	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12188070	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12188230	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12514091	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs12518849	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12520003	1.00[CEU][hapmap]
rs12521391	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12522683	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12522862	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12523027	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12523284	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13436236	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs17135454	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135463	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135488	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17135506	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135507	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135515	1.00[CEU][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135517	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135520	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17135526	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135531	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135534	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17135535	0.87[AMR][1000 genomes]
rs17135542	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs17135546	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17164185	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1822488	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1845289	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1850410	0.85[CEU][hapmap];0.97[EUR][1000 genomes]
rs1997521	0.88[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2091803	0.88[JPT][hapmap]
rs34271294	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4632792	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705549	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705806	0.88[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4705807	0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4705808	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4705809	0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4705810	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56294433	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56362568	0.82[AFR][1000 genomes]
rs59107004	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs59222257	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs60087454	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs60437559	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594695	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594696	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594697	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66893265	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs67063423	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs67373655	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs67550282	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs68069850	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6879761	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6887565	0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6888602	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs73244759	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73244767	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73244768	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73244769	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73244770	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73244772	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73244779	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73246604	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73246629	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73246681	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7703865	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7707127	0.94[YRI][hapmap]
rs7724707	0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7724717	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7724936	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs971370	0.82[AMR][1000 genomes]
rs971371	0.82[AMR][1000 genomes]
rs971373	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
3	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:112589200-112610600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:112598800-112603800	Enhancers	Liver	Liver
6	chr5:112599400-112603000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr5:112599800-112604800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:112600200-112604800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:112600200-112605000	Weak transcription	NH-A	brain
10	chr5:112600200-112618000	Weak transcription	Fetal Kidney	kidney
11	chr5:112600400-112605200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:112600800-112602800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr5:112600800-112602800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr5:112600800-112605000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:112600800-112607200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:112600800-112607600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:112600800-112608000	Enhancers	Ovary	ovary
18	chr5:112600800-112610600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:112600800-112610800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:112601000-112602600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:112601000-112603400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr5:112601000-112604000	Enhancers	Fetal Heart	heart
23	chr5:112601000-112606200	Enhancers	Right Atrium	heart
24	chr5:112601000-112612400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr5:112601200-112603800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr5:112601200-112605000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:112601200-112605800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:112601400-112611200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr5:112601800-112602600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:112602000-112602800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:112602000-112603000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:112602000-112603000	Enhancers	Brain Substantia Nigra	brain
33	chr5:112602000-112603400	Enhancers	Adipose Nuclei	Adipose
34	chr5:112602000-112603600	Enhancers	Psoas Muscle	Psoas
35	chr5:112602000-112605000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:112602200-112602600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:112602200-112603000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:112602200-112603000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:112602200-112603000	Enhancers	Placenta	Placenta
40	chr5:112602200-112603000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:112602200-112603200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:112602200-112604000	Enhancers	Esophagus	oesophagus
43	chr5:112602200-112604000	Enhancers	Left Ventricle	heart
44	chr5:112602200-112604000	Flanking Active TSS	NHEK	skin
45	chr5:112602200-112604200	Enhancers	Right Ventricle	heart
46	chr5:112602200-112606600	Weak transcription	Fetal Lung	lung
47	chr5:112602200-112616600	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:112602400-112602600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:112602400-112602600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:112602400-112603400	Flanking Active TSS	HMEC	breast

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