Variant report

Variant	rs1496336
Chromosome Location	chr5:92414492-92414493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:92405044..92407618-chr5:92412622..92415093,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1027429	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1027430	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10514368	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10514369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1075873	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11951873	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11958890	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12514052	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12514544	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12515643	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12523622	0.98[ASN][1000 genomes]
rs1390614	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1496338	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496339	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1496341	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1603407	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17082878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17082886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1845837	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1845838	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1845839	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1961168	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017806	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132535	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2173008	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2342063	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2438470	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578487	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2578488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2578489	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2578491	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578492	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2578493	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644787	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34524	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3925782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4301219	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56993733	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57308733	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58430736	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59564433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59998698	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60548086	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6557059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67020389	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67939833	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68112398	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6861529	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6866281	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6870541	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7732596	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735078	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9314229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9314230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990959	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs991235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs995626	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998492	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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	nsv1015770	chr5:91911877-92498264	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1022712	chr5:92191693-92415111	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1028930	chr5:92194772-92415111	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv830399	chr5:92290915-92462490	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92413000-92415200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr5:92413000-92415800	Enhancers	HSMMtube	muscle
3	chr5:92413200-92414600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:92413200-92415200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:92413200-92415200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:92413400-92414800	Flanking Active TSS	GM12878-XiMat	blood
7	chr5:92413400-92415000	Enhancers	Ovary	ovary
8	chr5:92413800-92414600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:92413800-92414600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:92413800-92414600	Flanking Active TSS	Osteobl	bone
11	chr5:92413800-92415000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:92413800-92415000	Flanking Active TSS	NH-A	brain
13	chr5:92413800-92415200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:92413800-92415200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:92413800-92415200	Enhancers	Fetal Heart	heart
16	chr5:92414000-92414600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:92414000-92414600	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr5:92414000-92414600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr5:92414000-92415000	Enhancers	Fetal Kidney	kidney
20	chr5:92414000-92415000	Flanking Active TSS	HUVEC	blood vessel
21	chr5:92414000-92415200	Enhancers	Adipose Nuclei	Adipose
22	chr5:92414000-92415200	Enhancers	Right Atrium	heart
23	chr5:92414000-92415200	Enhancers	NHEK	skin
24	chr5:92414200-92414600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:92414200-92414600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:92414200-92414600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:92414200-92414600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:92414200-92414600	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr5:92414200-92414600	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr5:92414200-92414600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr5:92414200-92414600	Enhancers	Fetal Brain Male	brain
32	chr5:92414200-92414600	Enhancers	Fetal Brain Female	brain
33	chr5:92414200-92414600	Flanking Active TSS	Fetal Lung	lung
34	chr5:92414200-92414600	Enhancers	Fetal Stomach	stomach
35	chr5:92414200-92414600	Enhancers	Pancreas	Pancrea
36	chr5:92414200-92414600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr5:92414200-92414600	Enhancers	Small Intestine	intestine
38	chr5:92414200-92414600	Enhancers	Stomach Smooth Muscle	stomach
39	chr5:92414200-92414600	Flanking Active TSS	NHLF	lung
40	chr5:92414200-92414800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:92414200-92414800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:92414200-92414800	Active TSS	A549	lung
43	chr5:92414200-92414800	Flanking Active TSS	Hela-S3	cervix
44	chr5:92414200-92415000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:92414200-92415000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:92414200-92415000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:92414200-92415000	Enhancers	Fetal Muscle Leg	muscle
48	chr5:92414200-92415000	Flanking Active TSS	HepG2	liver
49	chr5:92414200-92415000	Flanking Active TSS	HMEC	breast
50	chr5:92414400-92414600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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