Variant report

Variant	rs2546116
Chromosome Location	chr5:112095332-112095333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111881640..111883991-chr5:112093471..112095416,2	K562	blood:
2	chr5:112043154..112046059-chr5:112093906..112095470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251014	Chromatin interaction
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10463643	0.81[EUR][1000 genomes]
rs1441375	0.85[EUR][1000 genomes]
rs1661035	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1661036	0.89[EUR][1000 genomes]
rs1734243	0.85[EUR][1000 genomes]
rs1816769	0.92[ASN][1000 genomes]
rs187075	0.88[EUR][1000 genomes]
rs1966477	0.87[EUR][1000 genomes]
rs2439591	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2464805	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545159	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2545162	0.86[EUR][1000 genomes]
rs2545163	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2545164	0.81[EUR][1000 genomes]
rs2545165	0.81[EUR][1000 genomes]
rs2545169	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2546111	0.88[EUR][1000 genomes]
rs2952615	0.82[EUR][1000 genomes]
rs351771	0.82[EUR][1000 genomes]
rs386830	0.85[EUR][1000 genomes]
rs392907	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs395266	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs397768	0.85[EUR][1000 genomes]
rs401908	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41115	0.81[EUR][1000 genomes]
rs411356	0.87[EUR][1000 genomes]
rs433429	0.85[EUR][1000 genomes]
rs458967	0.88[EUR][1000 genomes]
rs464002	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs464708	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs468179	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs501250	0.81[EUR][1000 genomes]
rs529076	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs563556	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs866006	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112074400-112095600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:112074400-112095600	Weak transcription	Fetal Thymus	thymus
3	chr5:112074400-112095800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:112074400-112102800	Weak transcription	Fetal Stomach	stomach
5	chr5:112074400-112103400	Weak transcription	Left Ventricle	heart
6	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:112074600-112103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:112074800-112097600	Weak transcription	HMEC	breast
11	chr5:112075200-112103000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:112075400-112097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:112075400-112101600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:112075600-112095600	Weak transcription	Dnd41	blood
15	chr5:112075600-112095800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:112076000-112095400	Weak transcription	NH-A	brain
17	chr5:112076200-112097000	Weak transcription	NHLF	lung
18	chr5:112078000-112095800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:112078600-112095800	Weak transcription	GM12878-XiMat	blood
20	chr5:112078800-112097200	Weak transcription	NHDF-Ad	bronchial
21	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:112079800-112095600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
24	chr5:112080200-112095800	Weak transcription	K562	blood
25	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:112084400-112103000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:112084600-112103200	Weak transcription	Psoas Muscle	Psoas
28	chr5:112084800-112101000	Weak transcription	Pancreas	Pancrea
29	chr5:112086600-112095600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:112087200-112098200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr5:112087600-112117600	Weak transcription	Gastric	stomach
32	chr5:112088200-112095400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:112088200-112095800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:112088600-112095600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:112089200-112095800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:112089400-112095800	Weak transcription	Fetal Lung	lung
37	chr5:112089400-112099400	Weak transcription	Fetal Intestine Large	intestine
38	chr5:112089800-112095600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:112089800-112095800	Weak transcription	HSMMtube	muscle
40	chr5:112089800-112116600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:112090000-112095400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:112090000-112097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:112090400-112095600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:112090400-112098400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:112091200-112097800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:112091400-112095800	Weak transcription	Primary T cells from cord blood	blood
47	chr5:112091400-112095800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr5:112091800-112095800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr5:112091800-112095800	Weak transcription	Fetal Brain Female	brain
50	chr5:112092800-112097800	Weak transcription	Fetal Brain Male	brain

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