Variant report

Variant	rs9506240
Chromosome Location	chr13:30476843-30476844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30475471..30478069-chr13:30488763..30491308,2	MCF-7	breast:
2	chr13:30421712..30424673-chr13:30474414..30478013,4	MCF-7	breast:
3	chr13:30421587..30425867-chr13:30475246..30480026,6	MCF-7	breast:
4	chr13:30475291..30479868-chr13:30496674..30499474,5	MCF-7	breast:
5	chr13:30474897..30477785-chr13:30478687..30482625,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10444626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12865275	0.85[EUR][1000 genomes]
rs7994728	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9314987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9506237	0.85[EUR][1000 genomes]
rs9506241	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9508586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9508587	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9508588	0.83[AMR][1000 genomes];1.00[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	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30475400-30480600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr13:30475600-30477200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:30475600-30477200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:30475600-30478600	Enhancers	HSMMtube	muscle
5	chr13:30475800-30477000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:30475800-30477000	Enhancers	HMEC	breast
7	chr13:30475800-30477000	Flanking Active TSS	NHEK	skin
8	chr13:30475800-30477600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:30475800-30477600	Enhancers	HSMM	muscle
10	chr13:30475800-30478000	Enhancers	Colonic Mucosa	Colon
11	chr13:30475800-30478600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr13:30476000-30477000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr13:30476000-30477000	Enhancers	Stomach Mucosa	stomach
14	chr13:30476000-30477200	Enhancers	NHLF	lung
15	chr13:30476000-30477400	Enhancers	Small Intestine	intestine
16	chr13:30476000-30477600	Enhancers	Placenta	Placenta
17	chr13:30476200-30477000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:30476200-30477000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:30476200-30477000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:30476200-30477000	Enhancers	Brain Substantia Nigra	brain
21	chr13:30476200-30477000	Flanking Active TSS	Hela-S3	cervix
22	chr13:30476200-30477200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:30476200-30477200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:30476200-30477200	Enhancers	Brain Cingulate Gyrus	brain
25	chr13:30476200-30477600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:30476400-30477000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr13:30476400-30477000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr13:30476400-30477000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr13:30476400-30477000	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr13:30476400-30477000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr13:30476400-30477000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr13:30476400-30477000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr13:30476400-30477000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr13:30476400-30477000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:30476400-30477000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr13:30476400-30477000	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr13:30476400-30477000	Enhancers	Fetal Thymus	thymus
38	chr13:30476400-30477000	Enhancers	Ovary	ovary
39	chr13:30476400-30477000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr13:30476400-30477000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr13:30476400-30477000	Enhancers	Thymus	Thymus
42	chr13:30476400-30477000	Enhancers	Dnd41	blood
43	chr13:30476400-30477200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr13:30476400-30477200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr13:30476400-30477200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:30476400-30477200	Enhancers	Brain Angular Gyrus	brain
47	chr13:30476400-30477200	Enhancers	Fetal Stomach	stomach
48	chr13:30476400-30477400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr13:30476400-30478200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:30476600-30477000	Enhancers	HUES6 Cell Line	embryonic stem cell

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