Variant report

Variant	rs1408655
Chromosome Location	chr13:79969988-79969989
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:79967156..79970145-chr13:79977393..79982048,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139746	Chromatin interaction
ENSG00000227354	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1324872	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1328043	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1328044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1328045	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1335376	1.00[AMR][1000 genomes]
rs1359411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1410330	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1410331	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1410333	0.90[AFR][1000 genomes]
rs1555731	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1571322	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1590466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1749987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1752645	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1853721	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1856995	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1885817	1.00[AMR][1000 genomes]
rs1980882	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2147567	1.00[AMR][1000 genomes]
rs2208944	1.00[AMR][1000 genomes]
rs2265032	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2484341	1.00[AMR][1000 genomes]
rs2484342	1.00[AMR][1000 genomes]
rs2760109	1.00[AMR][1000 genomes]
rs2760110	1.00[AMR][1000 genomes]
rs2765081	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2783128	1.00[AMR][1000 genomes]
rs2991462	1.00[AMR][1000 genomes]
rs314691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314696	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314698	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314699	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3861140	1.00[ASN][1000 genomes]
rs4052508	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs418177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4300513	1.00[AMR][1000 genomes]
rs450755	1.00[AMR][1000 genomes]
rs4884128	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4885630	1.00[AMR][1000 genomes]
rs6563092	1.00[AMR][1000 genomes]
rs6563099	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6563101	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563102	1.00[AMR][1000 genomes]
rs6563103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563118	1.00[AMR][1000 genomes]
rs7324585	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7325232	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7326625	1.00[ASN][1000 genomes]
rs7333651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7334029	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7334978	1.00[ASN][1000 genomes]
rs73566469	1.00[ASN][1000 genomes]
rs7993115	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7993478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7994560	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7996740	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7996869	1.00[AMR][1000 genomes]
rs7998224	1.00[AMR][1000 genomes]
rs8001089	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8001822	1.00[AMR][1000 genomes]
rs927696	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9318630	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9318631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9318637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9530903	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545056	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9545084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9545096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9601212	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:79951200-79979200	Weak transcription	Esophagus	oesophagus
2	chr13:79951800-79978200	Weak transcription	Aorta	Aorta
3	chr13:79952600-79977800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:79958600-79971000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:79958800-79971000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:79958800-79977800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr13:79960600-79975600	Weak transcription	Ovary	ovary
8	chr13:79960800-79971400	Weak transcription	NHLF	lung
9	chr13:79961600-79970000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr13:79962800-79973000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr13:79962800-79974400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr13:79967200-79970000	Strong transcription	A549	lung
13	chr13:79967600-79970000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr13:79967600-79972000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr13:79967800-79970000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr13:79967800-79970000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:79967800-79970000	ZNF genes & repeats	Fetal Stomach	stomach
18	chr13:79967800-79970400	Strong transcription	HSMM	muscle
19	chr13:79967800-79971000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:79968000-79970000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:79968000-79970200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:79968000-79970600	Weak transcription	NHDF-Ad	bronchial
23	chr13:79968000-79972800	Weak transcription	NHEK	skin
24	chr13:79968000-79973000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr13:79968000-79975200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:79968000-79975800	Weak transcription	HMEC	breast
27	chr13:79968000-79976600	Weak transcription	Right Ventricle	heart
28	chr13:79968000-79977800	Weak transcription	Gastric	stomach
29	chr13:79968200-79970000	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr13:79968200-79972800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr13:79968200-79973400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr13:79968200-79974400	Weak transcription	Brain Angular Gyrus	brain
33	chr13:79968200-79974600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:79968200-79975600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr13:79968400-79970000	Weak transcription	Brain Anterior Caudate	brain
36	chr13:79968400-79970000	Weak transcription	Fetal Heart	heart
37	chr13:79968400-79971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:79968400-79971800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr13:79968400-79972800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:79968400-79975800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr13:79968400-79977200	Weak transcription	Right Atrium	heart
42	chr13:79968400-79979200	Weak transcription	Lung	lung
43	chr13:79968600-79970000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr13:79968600-79970800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr13:79968600-79973000	Weak transcription	Adipose Nuclei	Adipose
46	chr13:79968600-79973000	Weak transcription	Liver	Liver
47	chr13:79968600-79973000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr13:79968600-79975600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr13:79968600-79976600	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:79968600-79977800	Weak transcription	Spleen	Spleen

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