Variant report

Variant	rs2439591
Chromosome Location	chr5:112089480-112089481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10073398	0.96[ASN][1000 genomes]
rs10463643	0.84[CHD][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1069061	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs1093677	0.83[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs11954856	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12513804	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12659119	0.96[ASN][1000 genomes]
rs12719151	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs1441375	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1465910	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs151976	0.82[CEU][hapmap]
rs151977	0.84[CEU][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap]
rs1661035	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1661036	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1734243	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs187075	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1966477	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2020383	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2229992	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs2431238	1.00[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs2464805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2545159	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2545162	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2545163	0.96[CEU][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2545164	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2545165	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2545166	0.83[CEU][hapmap]
rs2545167	0.83[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap]
rs2545169	0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2546110	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs2546111	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2546116	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2909786	0.93[CHB][hapmap]
rs2909787	0.93[CHB][hapmap]
rs2909958	0.93[CHB][hapmap]
rs2952615	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs351771	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs372492	0.84[CEU][hapmap]
rs382260	0.84[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs3846716	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs386830	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs392907	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs395266	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs397768	0.88[EUR][1000 genomes]
rs401908	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4099181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41115	0.85[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs411356	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs42427	0.85[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs429427	0.84[CHD][hapmap];0.84[GIH][hapmap]
rs430665	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs431287	0.84[CEU][hapmap]
rs433429	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs434157	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs458967	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs463229	0.84[CEU][hapmap]
rs464002	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs464708	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs465454	0.84[CHD][hapmap]
rs465899	0.85[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs468179	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs469727	0.87[GIH][hapmap];0.80[MEX][hapmap]
rs469760	0.83[CEU][hapmap]
rs4705609	0.82[ASN][1000 genomes]
rs4705815	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4705816	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs497844	0.84[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap]
rs501250	0.85[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs529076	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs544243	0.87[MEX][hapmap]
rs563556	0.92[CEU][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6594643	0.86[JPT][hapmap]
rs6594644	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6864688	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6867243	0.96[ASN][1000 genomes]
rs6894351	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs6898133	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs698405	0.87[GIH][hapmap];0.80[MEX][hapmap]
rs712662	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs712665	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs712668	0.84[CEU][hapmap]
rs818427	0.84[CEU][hapmap]
rs861674	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs866006	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs9326862	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][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:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112074000-112095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:112074200-112093200	Weak transcription	Aorta	Aorta
3	chr5:112074400-112090400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr5:112074400-112090400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:112074400-112091000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:112074400-112093200	Weak transcription	Right Ventricle	heart
7	chr5:112074400-112094000	Weak transcription	Fetal Intestine Small	intestine
8	chr5:112074400-112095200	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:112074400-112095600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:112074400-112095600	Weak transcription	Fetal Thymus	thymus
11	chr5:112074400-112095800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:112074400-112102800	Weak transcription	Fetal Stomach	stomach
13	chr5:112074400-112103400	Weak transcription	Left Ventricle	heart
14	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:112074600-112090400	Weak transcription	Primary B cells from cord blood	blood
18	chr5:112074600-112103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:112074800-112097600	Weak transcription	HMEC	breast
20	chr5:112075000-112093000	Weak transcription	Liver	Liver
21	chr5:112075000-112095200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:112075200-112092600	Weak transcription	HSMM	muscle
23	chr5:112075200-112094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:112075200-112103000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:112075400-112091000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:112075400-112097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:112075400-112101600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:112075600-112095600	Weak transcription	Dnd41	blood
29	chr5:112075600-112095800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:112076000-112090800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:112076000-112095400	Weak transcription	NH-A	brain
32	chr5:112076200-112097000	Weak transcription	NHLF	lung
33	chr5:112078000-112095800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:112078400-112091200	Weak transcription	Primary T cells from cord blood	blood
35	chr5:112078600-112093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:112078600-112095800	Weak transcription	GM12878-XiMat	blood
37	chr5:112078800-112092000	Weak transcription	Fetal Brain Male	brain
38	chr5:112078800-112097200	Weak transcription	NHDF-Ad	bronchial
39	chr5:112079000-112090600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:112079800-112095600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
43	chr5:112080200-112090600	Weak transcription	Fetal Brain Female	brain
44	chr5:112080200-112095800	Weak transcription	K562	blood
45	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr5:112083800-112091000	Weak transcription	Brain Germinal Matrix	brain
47	chr5:112084400-112103000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:112084600-112092800	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:112084600-112095200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:112084600-112103200	Weak transcription	Psoas Muscle	Psoas

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