Variant report

Variant	rs17135546
Chromosome Location	chr5:112616854-112616855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112616654..112618757-chr5:112626610..112628435,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10077020	0.83[AMR][1000 genomes]
rs10428666	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10519343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10519345	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10519346	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740045	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11740190	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740233	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740318	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740443	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11741794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741937	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11743052	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11744606	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs11746532	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11746791	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11746821	0.90[ASN][1000 genomes]
rs11748058	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11748465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11748503	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11748524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749864	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12186466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12188069	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12188070	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12188230	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12514091	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs12518849	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12520003	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12521391	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12522683	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12522862	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12523027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12523255	0.82[JPT][hapmap]
rs12523284	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13360719	0.85[AMR][1000 genomes]
rs13436236	0.85[JPT][hapmap]
rs1443683	0.83[AMR][1000 genomes]
rs17135454	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs17135463	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs17135488	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs17135506	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135507	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135514	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17135515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17135517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17135519	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17135520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135534	0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17135535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17135542	0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17135543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17164185	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs1822488	0.85[JPT][hapmap]
rs1838208	0.84[AMR][1000 genomes]
rs1845289	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1850410	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs1997521	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2068923	0.83[AMR][1000 genomes]
rs2091803	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2091804	0.83[ASN][1000 genomes]
rs34271294	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4632792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705549	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705806	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4705807	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4705808	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4705809	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4705810	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705811	0.84[ASN][1000 genomes]
rs4705817	0.85[JPT][hapmap]
rs56294433	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59107004	0.87[ASN][1000 genomes]
rs59222257	0.87[ASN][1000 genomes]
rs60087454	0.87[ASN][1000 genomes]
rs60437559	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6594695	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6594696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6594697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66893265	0.87[ASN][1000 genomes]
rs67063423	0.87[ASN][1000 genomes]
rs67373655	0.87[ASN][1000 genomes]
rs67550282	0.87[ASN][1000 genomes]
rs68069850	0.87[ASN][1000 genomes]
rs6879761	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6887565	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs6888602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs73244759	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73244767	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73244770	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73244772	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73244779	0.87[ASN][1000 genomes]
rs73246604	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73246629	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73246648	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73246657	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73246677	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73246681	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7703865	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7724707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7724717	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7724936	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs971370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs971371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs971373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs977997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:112600200-112618000	Weak transcription	Fetal Kidney	kidney
4	chr5:112608000-112628200	Weak transcription	HMEC	breast
5	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:112611000-112618000	Weak transcription	Fetal Stomach	stomach
8	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:112611200-112618000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:112612000-112618000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:112612000-112623800	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:112612000-112625200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:112612200-112617000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:112612200-112625200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:112612400-112617000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:112612400-112617000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:112612400-112618400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:112612600-112617200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:112613400-112618000	Enhancers	Ovary	ovary
20	chr5:112613600-112617200	Enhancers	Left Ventricle	heart
21	chr5:112614200-112617000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:112614200-112625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:112614400-112617000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:112614400-112617400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:112615000-112617200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:112615000-112625200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:112615200-112617400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:112615400-112617400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:112615600-112617200	Enhancers	Right Atrium	heart
30	chr5:112615800-112617200	Enhancers	Right Ventricle	heart
31	chr5:112616000-112617000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:112616400-112617000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:112616400-112617000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr5:112616400-112617200	Enhancers	Brain Substantia Nigra	brain
35	chr5:112616400-112617200	Enhancers	NH-A	brain
36	chr5:112616400-112617200	Enhancers	Osteobl	bone
37	chr5:112616400-112617600	Enhancers	HUVEC	blood vessel
38	chr5:112616400-112617800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr5:112616400-112618400	Enhancers	Adipose Nuclei	Adipose
40	chr5:112616400-112619000	Enhancers	Liver	Liver
41	chr5:112616400-112619200	Enhancers	Brain Anterior Caudate	brain
42	chr5:112616600-112617200	Enhancers	Psoas Muscle	Psoas
43	chr5:112616600-112618000	Enhancers	Brain Hippocampus Middle	brain
44	chr5:112616600-112618000	Weak transcription	Spleen	Spleen
45	chr5:112616600-112618400	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr5:112616600-112618400	Enhancers	Stomach Smooth Muscle	stomach
47	chr5:112616600-112620000	Enhancers	Fetal Heart	heart
48	chr5:112616800-112617400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:112616800-112617400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr5:112616800-112618000	Weak transcription	Brain Cingulate Gyrus	brain

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