Variant report

Variant	rs473909
Chromosome Location	chr13:30699444-30699445
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	chr13:30698648..30700274-chr13:30705836..30708500,2	MCF-7	breast:
2	chr13:30697642..30699768-chr13:30715433..30718388,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2388497	0.87[EUR][1000 genomes]
rs471343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472327	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480097	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs482983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559122	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs589064	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs597794	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs613712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs614220	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs614644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643621	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs656305	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7327238	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs913902	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040215	chr13:30621351-30741022	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541745	chr13:30621351-30741022	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30690200-30699800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:30694400-30699600	Weak transcription	NH-A	brain
3	chr13:30694400-30699800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr13:30694400-30707000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:30694600-30699600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:30694600-30699600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:30694600-30699600	Weak transcription	HSMM	muscle
8	chr13:30694600-30699600	Weak transcription	NHDF-Ad	bronchial
9	chr13:30694800-30699800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:30695000-30701000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr13:30696000-30699600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:30696400-30707000	Weak transcription	Thymus	Thymus
13	chr13:30696600-30702800	Weak transcription	Fetal Thymus	thymus
14	chr13:30697400-30699600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:30697800-30702200	Enhancers	Colon Smooth Muscle	Colon
16	chr13:30697800-30702600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr13:30698000-30699600	Weak transcription	Esophagus	oesophagus
18	chr13:30698200-30701800	Enhancers	Stomach Smooth Muscle	stomach
19	chr13:30698200-30702400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:30698400-30701600	Enhancers	Rectal Smooth Muscle	rectum
21	chr13:30698400-30701800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:30698800-30699800	Enhancers	Brain Cingulate Gyrus	brain
23	chr13:30699000-30699800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr13:30699200-30699800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:30699400-30700000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:30699400-30700000	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr13:30699400-30700000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr13:30699400-30700000	Enhancers	Hela-S3	cervix
29	chr13:30699400-30700200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:30699400-30700600	Enhancers	A549	lung
31	chr13:30699400-30700800	Enhancers	HMEC	breast
32	chr13:30699400-30701400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr13:30699400-30701400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr13:30699400-30701600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:30699400-30701800	Enhancers	NHLF	lung
36	chr13:30699400-30701800	Enhancers	Osteobl	bone
37	chr13:30699400-30702000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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