Variant report

Variant	rs13172960
Chromosome Location	chr5:52004558-52004559
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52002898..52006870-chr5:52009396..52011891,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13153693	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155491	0.80[AMR][1000 genomes]
rs13157816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13158962	0.88[AMR][1000 genomes]
rs13160140	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13161242	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162384	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13163634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165120	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13167330	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13168671	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13172827	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175042	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185633	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361161	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71633440	0.83[AMR][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	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 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	chr5:51992800-52005200	Weak transcription	Fetal Kidney	kidney
2	chr5:51998600-52008800	Enhancers	Primary T cells from cord blood	blood
3	chr5:51999600-52007000	Weak transcription	Psoas Muscle	Psoas
4	chr5:52000800-52009000	Enhancers	Dnd41	blood
5	chr5:52001200-52006600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:52001600-52005400	Enhancers	HepG2	liver
7	chr5:52001800-52005400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:52002000-52005000	Weak transcription	NHEK	skin
9	chr5:52002200-52005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:52002200-52007600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:52002400-52004600	Weak transcription	NHDF-Ad	bronchial
12	chr5:52002400-52005000	Weak transcription	HSMM	muscle
13	chr5:52002400-52008200	Enhancers	Small Intestine	intestine
14	chr5:52002600-52005000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:52002600-52005000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:52002600-52005000	Weak transcription	HSMMtube	muscle
17	chr5:52002600-52005600	Weak transcription	Left Ventricle	heart
18	chr5:52002800-52005000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:52002800-52005200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:52003000-52005400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr5:52003000-52005400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:52003000-52005400	Weak transcription	Fetal Thymus	thymus
23	chr5:52003000-52005600	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:52003000-52007800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:52003800-52005400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:52003800-52005800	Enhancers	Duodenum Mucosa	Duodenum
27	chr5:52003800-52006200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:52003800-52007200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:52004000-52004600	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr5:52004000-52005600	Enhancers	NH-A	brain
31	chr5:52004000-52005800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:52004000-52006400	Weak transcription	Spleen	Spleen
33	chr5:52004000-52007600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr5:52004000-52007600	Enhancers	Osteobl	bone
35	chr5:52004200-52005200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:52004200-52005800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:52004200-52005800	Enhancers	HUVEC	blood vessel
38	chr5:52004200-52006400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr5:52004200-52007400	Enhancers	NHLF	lung
40	chr5:52004400-52004800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:52004400-52006000	Enhancers	Primary hematopoietic stem cells	blood
42	chr5:52004400-52006000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr5:52004400-52006200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:52004400-52007000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:52004400-52007200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr5:52004400-52007400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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