Variant report

Variant	rs9534969
Chromosome Location	chr13:48727389-48727390
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48719328..48721688-chr13:48725913..48727426,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1749976	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925747	0.86[ASN][1000 genomes]
rs2182220	0.86[ASN][1000 genomes]
rs2406802	0.84[ASN][1000 genomes]
rs2406804	0.84[ASN][1000 genomes]
rs2765074	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2765075	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942753	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4942754	0.87[ASN][1000 genomes]
rs4942757	0.84[ASN][1000 genomes]
rs607954	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7329629	0.86[ASN][1000 genomes]
rs7988534	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7989671	0.86[ASN][1000 genomes]
rs7993868	0.84[ASN][1000 genomes]
rs7994141	0.84[ASN][1000 genomes]
rs7995410	0.87[ASN][1000 genomes]
rs9534978	0.88[ASN][1000 genomes]
rs9534979	0.87[ASN][1000 genomes]
rs9534983	0.86[ASN][1000 genomes]
rs9534988	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48717400-48733200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:48721600-48727600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr13:48722400-48730600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr13:48722600-48730000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr13:48722800-48729800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:48723200-48730600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr13:48723800-48730400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr13:48724200-48738200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr13:48725200-48727800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:48725400-48728200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:48725600-48727400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:48725600-48727600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:48725800-48727400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:48726000-48727400	Enhancers	Primary T cells from cord blood	blood
15	chr13:48726200-48727400	Enhancers	Primary B cells from cord blood	blood
16	chr13:48726200-48727800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr13:48726200-48729400	Weak transcription	Fetal Thymus	thymus
18	chr13:48726200-48729400	Weak transcription	Dnd41	blood
19	chr13:48726200-48730000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr13:48726200-48731600	Enhancers	Placenta	Placenta
21	chr13:48726400-48727400	Weak transcription	NHEK	skin
22	chr13:48726400-48727800	Weak transcription	HMEC	breast
23	chr13:48726400-48729800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr13:48726400-48729800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr13:48726400-48730000	Weak transcription	GM12878-XiMat	blood
26	chr13:48726400-48730200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr13:48726400-48730400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:48726400-48733600	Weak transcription	Esophagus	oesophagus
29	chr13:48726400-48735400	Weak transcription	Lung	lung
30	chr13:48726600-48727400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr13:48726600-48727600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr13:48726600-48728800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr13:48726600-48731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:48726600-48732000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr13:48726800-48727800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr13:48726800-48728800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr13:48726800-48728800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr13:48726800-48728800	Weak transcription	Adipose Nuclei	Adipose
39	chr13:48726800-48728800	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr13:48726800-48730000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr13:48726800-48730000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr13:48727000-48727400	Weak transcription	Small Intestine	intestine
43	chr13:48727000-48728400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr13:48727000-48728800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:48727200-48727800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr13:48727200-48728800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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