Variant report

Variant	rs541434
Chromosome Location	chr13:52371754-52371755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52358110..52360394-chr13:52370538..52373206,3	MCF-7	breast:
2	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
3	chr13:52352368..52355270-chr13:52370453..52372078,2	MCF-7	breast:
4	chr13:52008757..52009930-chr13:52371510..52372492,6	MCF-7	breast:
5	chr13:52157433..52159948-chr13:52371232..52373854,2	MCF-7	breast:
6	chr13:51871805..51872313-chr13:52371607..52372516,2	MCF-7	breast:
7	chr13:52370681..52375031-chr13:52376464..52379694,5	MCF-7	breast:
8	chr13:52368810..52370322-chr13:52370429..52372255,2	MCF-7	breast:
9	chr13:52025654..52028451-chr13:52369757..52372475,3	K562	blood:
10	chr13:52018821..52019828-chr13:52371557..52372566,3	MCF-7	breast:
11	chr13:52008831..52009730-chr13:52371598..52372485,2	MCF-7	breast:
12	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
13	chr13:52307647..52308183-chr13:52371468..52372047,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000231856	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2734	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760302	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2760303	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2760304	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760305	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2773267	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2773268	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773269	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471107	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs512948	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs518210	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs732004	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535761	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv1840020	chr13:52345838-52388765	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52339600-52375000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr13:52339800-52375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr13:52344600-52371800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:52346400-52376000	Weak transcription	Thymus	Thymus
5	chr13:52348200-52375600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr13:52348200-52375600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:52358000-52372000	Weak transcription	HepG2	liver
8	chr13:52358600-52375600	Weak transcription	Colonic Mucosa	Colon
9	chr13:52359000-52375600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr13:52360400-52373600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:52360600-52376000	Weak transcription	Gastric	stomach
12	chr13:52360800-52375600	Weak transcription	Fetal Intestine Large	intestine
13	chr13:52361000-52374800	Weak transcription	Stomach Mucosa	stomach
14	chr13:52361000-52375600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr13:52361400-52373200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:52361600-52372200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:52361600-52374400	Weak transcription	Colon Smooth Muscle	Colon
18	chr13:52361600-52374400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr13:52361600-52374600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:52361600-52374600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr13:52361600-52375000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr13:52361600-52375800	Weak transcription	Brain Germinal Matrix	brain
23	chr13:52361600-52376400	Weak transcription	Fetal Brain Female	brain
24	chr13:52361800-52374400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr13:52361800-52374600	Weak transcription	Psoas Muscle	Psoas
26	chr13:52361800-52376200	Weak transcription	Fetal Brain Male	brain
27	chr13:52363200-52374600	Weak transcription	Left Ventricle	heart
28	chr13:52364000-52374600	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:52364000-52374800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr13:52364200-52375800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr13:52366000-52375800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr13:52367200-52372400	Enhancers	Pancreas	Pancrea
33	chr13:52367400-52373600	Weak transcription	Brain Substantia Nigra	brain
34	chr13:52367800-52374400	Weak transcription	Brain Anterior Caudate	brain
35	chr13:52368000-52373600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr13:52368000-52373800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr13:52368200-52372000	Strong transcription	Fetal Intestine Small	intestine
38	chr13:52368200-52372200	Weak transcription	NHEK	skin
39	chr13:52368200-52377000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:52368400-52371800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:52368400-52375600	Weak transcription	HSMMtube	muscle
42	chr13:52368400-52375800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr13:52368400-52376000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr13:52368600-52372000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:52368600-52373600	Strong transcription	Fetal Muscle Leg	muscle
46	chr13:52368600-52375800	Weak transcription	Esophagus	oesophagus
47	chr13:52368800-52375800	Weak transcription	Fetal Thymus	thymus
48	chr13:52369000-52372000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:52369000-52373200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr13:52369400-52375800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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