Variant report

Variant	rs17135515
Chromosome Location	chr5:112598947-112598948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112595001..112597211-chr5:112597744..112599489,3	MCF-7	breast:
2	chr5:112597661..112600348-chr5:112601306..112603277,2	MCF-7	breast:
3	chr5:112566555..112568778-chr5:112596838..112599414,2	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10428666	0.92[EUR][1000 genomes]
rs10519343	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10519345	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs10519346	0.90[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1116547	0.95[MEX][hapmap]
rs11241197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11241201	0.95[MEX][hapmap]
rs11241206	0.90[MEX][hapmap]
rs11738215	0.90[MEX][hapmap]
rs11740045	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11740190	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740233	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740318	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740443	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11741937	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11743052	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11744606	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11746532	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11746791	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11746821	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11748058	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11748503	0.92[EUR][1000 genomes]
rs11748524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11749864	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12186466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188069	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188070	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188230	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12514091	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs12518849	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12520003	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12521391	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12522683	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12522862	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12523027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12523284	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13360719	0.80[AMR][1000 genomes]
rs17135454	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135463	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17135488	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17135506	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135507	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135514	1.00[CEU][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17135517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135519	1.00[CEU][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135534	0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs17135535	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17135543	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17135546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17164185	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1845289	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1850410	0.85[CEU][hapmap];0.97[EUR][1000 genomes]
rs1997521	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2068923	1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2091803	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2091804	0.93[ASN][1000 genomes]
rs34271294	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3846721	0.81[MEX][hapmap]
rs4632792	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705549	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4705807	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4705808	1.00[CHB][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4705809	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4705810	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56294433	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56362568	0.85[ASN][1000 genomes]
rs59107004	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59222257	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60087454	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60437559	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594695	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66893265	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67063423	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67373655	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67550282	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs68069850	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6864528	0.90[MEX][hapmap]
rs6877524	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs6879761	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879800	0.85[MEX][hapmap]
rs6887565	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6888602	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73244759	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73244767	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73244768	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73244769	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73244770	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73244772	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73244779	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73246604	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73246629	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73246648	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73246657	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73246677	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73246681	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7703865	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7707127	0.83[YRI][hapmap]
rs7724707	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7724717	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7724936	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs971370	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs971371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs971373	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs977997	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.85[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17135515	DCP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112582800-112601000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:112583600-112599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
5	chr5:112586800-112599400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:112587200-112599400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:112588000-112601200	Weak transcription	HMEC	breast
9	chr5:112589200-112610600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112589400-112602200	Weak transcription	Esophagus	oesophagus
11	chr5:112591600-112602000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:112593600-112599400	Weak transcription	Fetal Heart	heart
13	chr5:112593800-112599800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:112594400-112602200	Weak transcription	Left Ventricle	heart
15	chr5:112594400-112602200	Weak transcription	Right Ventricle	heart
16	chr5:112595200-112600800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:112595200-112601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:112595400-112599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:112595600-112599200	Weak transcription	NHEK	skin
20	chr5:112595600-112602200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:112597000-112599800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:112597000-112600800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:112598000-112600000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr5:112598400-112599600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:112598600-112599000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr5:112598600-112599000	Enhancers	Fetal Lung	lung
27	chr5:112598600-112600400	Enhancers	Ovary	ovary
28	chr5:112598600-112600800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:112598600-112601000	Weak transcription	Right Atrium	heart
30	chr5:112598600-112601200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:112598800-112599000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr5:112598800-112599200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr5:112598800-112600200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr5:112598800-112600200	Enhancers	Fetal Kidney	kidney
35	chr5:112598800-112600600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:112598800-112603800	Enhancers	Liver	Liver

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