Variant report

Variant	rs1043729
Chromosome Location	chr13:50273831-50273832
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	chr13:50272679..50274281-chr13:50397639..50400359,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12585921	0.84[EUR][1000 genomes]
rs13313256	0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17073322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17073347	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17073356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1819191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885723	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1969739	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1986085	0.84[EUR][1000 genomes]
rs1998363	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2181184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs3736830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3742094	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3782929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3903770	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs4941655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4941656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942862	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56738401	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57118905	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57783887	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57794226	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58124341	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60019803	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60106669	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60856213	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7318922	0.90[YRI][hapmap]
rs7321391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7334018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7335016	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7335310	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483835	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73485710	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs765291	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs765292	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7984711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7989633	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7990293	0.86[ASN][1000 genomes]
rs7993631	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7993860	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7994062	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7996015	0.89[YRI][hapmap]
rs8002212	0.90[YRI][hapmap]
rs9535306	0.97[ASN][1000 genomes]
rs9562911	0.95[JPT][hapmap]
rs9591288	0.81[YRI][hapmap]
rs9591293	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9591294	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9591296	0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9596166	0.95[JPT][hapmap]
rs9596172	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596181	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9596189	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9596194	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][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	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv819200	chr13:50272099-50274553	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
5	nsv983586	chr13:50273632-50274324	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266000-50278200	Weak transcription	Lung	lung
2	chr13:50266000-50284200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:50266200-50274200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:50266200-50274400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:50266200-50275000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr13:50266200-50275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:50266200-50275000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:50266200-50275000	Weak transcription	Fetal Brain Male	brain
9	chr13:50266200-50275000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr13:50266200-50275000	Weak transcription	Thymus	Thymus
11	chr13:50266200-50275000	Weak transcription	GM12878-XiMat	blood
12	chr13:50266200-50275000	Weak transcription	Hela-S3	cervix
13	chr13:50266200-50275000	Weak transcription	NHDF-Ad	bronchial
14	chr13:50266200-50275200	Weak transcription	Brain Hippocampus Middle	brain
15	chr13:50266200-50275200	Weak transcription	HSMMtube	muscle
16	chr13:50266200-50275400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr13:50266200-50275400	Weak transcription	Brain Substantia Nigra	brain
18	chr13:50266200-50275400	Weak transcription	Fetal Kidney	kidney
19	chr13:50266200-50275400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:50266200-50275400	Weak transcription	Right Ventricle	heart
21	chr13:50266200-50275400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:50266200-50275600	Weak transcription	Fetal Lung	lung
23	chr13:50266200-50279200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:50266200-50279400	Weak transcription	Brain Angular Gyrus	brain
25	chr13:50266200-50279400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr13:50266200-50282200	Weak transcription	Brain Germinal Matrix	brain
27	chr13:50266200-50285600	Weak transcription	NHLF	lung
28	chr13:50266200-50286000	Weak transcription	Psoas Muscle	Psoas
29	chr13:50266200-50289400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr13:50266200-50289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr13:50266200-50295200	Weak transcription	Spleen	Spleen
32	chr13:50266200-50296000	Weak transcription	K562	blood
33	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr13:50266200-50307800	Weak transcription	Gastric	stomach
36	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr13:50266400-50274000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:50266400-50274200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:50266400-50274200	Weak transcription	Fetal Thymus	thymus
40	chr13:50266400-50274400	Weak transcription	HepG2	liver
41	chr13:50266400-50274600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr13:50266400-50274800	Weak transcription	Primary B cells from cord blood	blood
43	chr13:50266400-50274800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr13:50266400-50274800	Weak transcription	HMEC	breast
45	chr13:50266400-50275000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr13:50266400-50275000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr13:50266400-50275000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr13:50266400-50275000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr13:50266400-50275000	Weak transcription	Brain Anterior Caudate	brain
50	chr13:50266400-50275000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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