Variant report

Variant	rs13404397
Chromosome Location	chr2:134399085-134399086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:134365245..134367451-chr2:134398214..134401016,3	MCF-7	breast:
2	chr2:134386454..134389246-chr2:134397997..134400619,2	MCF-7	breast:
3	chr2:134020041..134020759-chr2:134398921..134399467,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10165896	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10169733	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10171394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10177415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185005	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10185520	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192051	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10193288	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10193374	0.86[ASN][1000 genomes]
rs10193580	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10206506	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12328892	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13391014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13393385	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13404176	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13407575	0.93[ASN][1000 genomes]
rs13409971	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13412577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13416986	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419634	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13425366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429974	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13430360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13430590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16827735	0.86[ASN][1000 genomes]
rs1901428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901429	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901432	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901433	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993136	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1993137	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2084808	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2084809	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478058	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28514481	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55646124	0.86[ASN][1000 genomes]
rs57451360	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58763272	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59085210	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60598686	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62177769	0.86[ASN][1000 genomes]
rs62179347	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180296	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180299	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180300	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180302	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180303	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730046	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6733088	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748388	0.96[EUR][1000 genomes]
rs67792617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843232	0.86[ASN][1000 genomes]
rs7422753	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv2934	chr2:134368478-134412454	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv998920	chr2:134382097-134424640	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134395000-134399600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:134395800-134402800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:134397200-134399200	Active TSS	Brain Substantia Nigra	brain
4	chr2:134397200-134399200	Flanking Active TSS	NHEK	skin
5	chr2:134397600-134399400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:134397600-134402000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:134397800-134399200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:134397800-134399200	Active TSS	Brain Angular Gyrus	brain
9	chr2:134398400-134399200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr2:134398600-134401000	Enhancers	Osteobl	bone
11	chr2:134398800-134399400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:134398800-134399800	Enhancers	Placenta	Placenta
13	chr2:134398800-134400400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:134398800-134401800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:134398800-134402800	Enhancers	Brain Anterior Caudate	brain
16	chr2:134399000-134399200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:134399000-134399200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr2:134399000-134399200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr2:134399000-134399200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:134399000-134399200	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr2:134399000-134399200	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr2:134399000-134399200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr2:134399000-134399400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:134399000-134399400	Enhancers	Fetal Brain Male	brain
25	chr2:134399000-134399400	Enhancers	Fetal Muscle Trunk	muscle
26	chr2:134399000-134399400	Enhancers	Gastric	stomach
27	chr2:134399000-134399400	Enhancers	Left Ventricle	heart
28	chr2:134399000-134399400	Enhancers	Pancreas	Pancrea
29	chr2:134399000-134399400	Enhancers	Stomach Mucosa	stomach
30	chr2:134399000-134399400	Active TSS	HMEC	breast
31	chr2:134399000-134399800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:134399000-134399800	Enhancers	Esophagus	oesophagus
33	chr2:134399000-134400000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr2:134399000-134400000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:134399000-134400200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:134399000-134400400	Enhancers	Fetal Muscle Leg	muscle
37	chr2:134399000-134400600	Enhancers	NHLF	lung
38	chr2:134399000-134400800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:134399000-134401000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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