Variant report

Variant	rs13209830
Chromosome Location	chr6:131363318-131363319
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:131356533..131360824-chr6:131360872..131363958,3	MCF-7	breast:
2	chr6:131361605..131363567-chr6:131382712..131384609,2	MCF-7	breast:
3	chr6:131356781..131360402-chr6:131360756..131363630,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079819	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11154614	0.92[ASN][1000 genomes]
rs11961521	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11969461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12527232	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665101	0.89[ASN][1000 genomes]
rs12665208	0.81[ASN][1000 genomes]
rs13192526	0.81[ASN][1000 genomes]
rs13207929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332492	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338906	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17180547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1855078	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1977744	0.94[ASN][1000 genomes]
rs34445705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34863373	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35273150	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66491359	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6908768	0.94[ASN][1000 genomes]
rs6923182	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72987859	1.00[ASN][1000 genomes]
rs72987891	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72989827	0.92[ASN][1000 genomes]
rs72989829	0.92[ASN][1000 genomes]
rs7743764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745206	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9483209	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9492784	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492785	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492799	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131346000-131375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:131351400-131375000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:131351600-131374600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:131352400-131374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:131353800-131364000	Weak transcription	Ovary	ovary
6	chr6:131356600-131375000	Weak transcription	Brain Angular Gyrus	brain
7	chr6:131357400-131367200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:131359000-131374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:131360400-131365600	Weak transcription	Adipose Nuclei	Adipose
10	chr6:131360400-131367400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:131360600-131363400	Weak transcription	A549	lung
12	chr6:131360600-131367200	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:131360800-131364000	Enhancers	NHLF	lung
14	chr6:131360800-131364800	Enhancers	HepG2	liver
15	chr6:131360800-131368000	Weak transcription	Small Intestine	intestine
16	chr6:131360800-131370000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:131360800-131374800	Weak transcription	HSMM	muscle
18	chr6:131360800-131375000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:131361000-131367600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:131361400-131373800	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:131361600-131369000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:131362000-131363400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:131362000-131364000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:131362000-131364200	Enhancers	Osteobl	bone
25	chr6:131362200-131364400	Enhancers	Fetal Stomach	stomach
26	chr6:131362400-131364400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:131362800-131363800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:131362800-131364200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:131362800-131366600	Weak transcription	Brain Anterior Caudate	brain
30	chr6:131363200-131363400	Enhancers	NHDF-Ad	bronchial
31	chr6:131363200-131363600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:131363200-131364400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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