Variant report

Variant	rs4864862
Chromosome Location	chr4:55100489-55100490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:54774460..54775444-chr4:55099657..55101013,5	K562	blood:
2	chr4:53100125..53100934-chr4:55099670..55100577,2	K562	blood:
3	chr4:53849487..53850046-chr4:55100113..55100951,2	MCF-7	breast:
4	chr4:53881814..53882461-chr4:55099539..55100545,3	MCF-7	breast:
5	chr4:53881829..53882444-chr4:55100138..55101053,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11133315	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12505054	0.84[AFR][1000 genomes]
rs12505491	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12506290	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12506783	0.91[YRI][hapmap]
rs12508225	0.80[ASN][1000 genomes]
rs12641563	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12644709	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12644749	0.80[ASN][1000 genomes]
rs1565669	0.80[ASN][1000 genomes]
rs1565670	0.80[ASN][1000 genomes]
rs17084051	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800810	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1800812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800813	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229307	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2307049	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2307050	0.80[JPT][hapmap]
rs28528897	0.80[ASN][1000 genomes]
rs28600756	0.80[ASN][1000 genomes]
rs4358459	0.80[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4368668	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398585	0.86[AFR][1000 genomes]
rs4422471	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4608869	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864855	0.86[AFR][1000 genomes]
rs4864856	0.88[AFR][1000 genomes]
rs4864857	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864858	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864859	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864860	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864861	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864864	0.80[ASN][1000 genomes]
rs4864865	0.80[ASN][1000 genomes]
rs56145315	0.80[ASN][1000 genomes]
rs58435984	0.84[ASN][1000 genomes]
rs58727676	0.80[ASN][1000 genomes]
rs60806423	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60863210	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61320297	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554160	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6554163	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67279506	0.80[ASN][1000 genomes]
rs67432867	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67600360	0.80[ASN][1000 genomes]
rs6831380	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6832597	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6836215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6850748	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73252942	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73252946	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73252948	0.80[ASN][1000 genomes]
rs7660560	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7673027	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673267	0.82[AFR][1000 genomes]
rs7673597	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7673625	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673853	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7673984	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7676972	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7677751	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7678144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679903	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681399	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682912	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7683707	0.88[AFR][1000 genomes]
rs7686588	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7688997	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7689569	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690503	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7691129	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7698425	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs890203	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991165	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002905	chr4:55093677-55115698	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 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	chr4:55092000-55100800	Active TSS	Aorta	Aorta
2	chr4:55092400-55100600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:55093200-55100800	Active TSS	NHDF-Ad	bronchial
4	chr4:55093200-55102000	Active TSS	Ovary	ovary
5	chr4:55094200-55100800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:55094800-55100800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:55095000-55100600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:55095000-55100800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr4:55095600-55100600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr4:55096000-55100600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:55096000-55100800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:55096600-55100600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr4:55096600-55100600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:55096600-55101400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:55097400-55100600	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr4:55097400-55101200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:55098000-55101000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr4:55098400-55101200	Active TSS	Right Atrium	heart
19	chr4:55098400-55101400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:55098600-55100600	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr4:55098800-55100600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr4:55098800-55100600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:55098800-55101000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:55098800-55101000	Active TSS	A549	lung
25	chr4:55098800-55101200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:55099000-55100600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr4:55099000-55100600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:55099000-55100600	Flanking Active TSS	Liver	Liver
29	chr4:55099000-55100600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr4:55099000-55100600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr4:55099000-55101200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr4:55099000-55101200	Active TSS	Rectal Smooth Muscle	rectum
33	chr4:55099000-55101400	Active TSS	Fetal Kidney	kidney
34	chr4:55099200-55100600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
35	chr4:55099200-55100600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
36	chr4:55099200-55100600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr4:55099200-55100600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr4:55099200-55100600	Flanking Active TSS	Placenta	Placenta
39	chr4:55099200-55100600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
40	chr4:55099200-55100600	Flanking Active TSS	HMEC	breast
41	chr4:55099200-55100800	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr4:55099200-55100800	Active TSS	Fetal Lung	lung
43	chr4:55099200-55100800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr4:55099200-55101000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:55099200-55101200	Active TSS	Brain Angular Gyrus	brain
46	chr4:55099400-55100600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr4:55099400-55100600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr4:55099400-55100600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr4:55099400-55100600	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr4:55099400-55100600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle

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