Variant report

Variant	rs4688715
Chromosome Location	chr3:50553721-50553722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1077215	0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs1107312	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12486143	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12487817	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12489607	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12491440	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12491812	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12494094	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12494326	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12494707	0.92[AMR][1000 genomes]
rs17050991	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17050995	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17051000	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17051043	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17051045	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17051403	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs1872184	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1894459	0.95[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2035484	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2170840	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2227292	0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227293	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239750	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239751	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2239752	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2239753	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2285090	0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3749265	0.90[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3752449	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792323	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3806706	0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4640555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688705	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4688707	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4688709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4688710	0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4688713	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4688716	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56170012	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58427389	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs60552073	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61193866	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61316441	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61574029	0.98[ASN][1000 genomes]
rs61613532	0.98[ASN][1000 genomes]
rs616689	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6766638	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6771348	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs728902	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs72938758	0.98[ASN][1000 genomes]
rs73835531	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs743753	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs745356	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs762889	0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs808148	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs876103	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs876104	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs876105	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs9814874	0.86[CHB][hapmap]
rs9879397	0.89[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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 miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50551600-50555200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:50551800-50554200	Enhancers	Fetal Kidney	kidney
3	chr3:50551800-50554400	Enhancers	HSMMtube	muscle
4	chr3:50551800-50557600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:50552000-50553800	Enhancers	Fetal Lung	lung
6	chr3:50552200-50554800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:50552200-50555200	Enhancers	Fetal Heart	heart
8	chr3:50552200-50555800	Enhancers	Spleen	Spleen
9	chr3:50552200-50556600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:50552200-50557600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:50552400-50554000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:50552400-50555200	Enhancers	Placenta	Placenta
13	chr3:50552600-50553800	Enhancers	Brain Hippocampus Middle	brain
14	chr3:50552600-50553800	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr3:50552600-50554200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:50552600-50554200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:50552600-50554400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:50552600-50554400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:50552600-50554400	Enhancers	Brain Germinal Matrix	brain
20	chr3:50552600-50554600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr3:50552600-50554600	Enhancers	Primary B cells from cord blood	blood
22	chr3:50552600-50555200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:50552800-50553800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:50552800-50553800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:50552800-50553800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:50552800-50553800	Enhancers	Brain Anterior Caudate	brain
27	chr3:50552800-50554000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr3:50552800-50554000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr3:50552800-50554000	Enhancers	NH-A	brain
30	chr3:50552800-50554200	Enhancers	Lung	lung
31	chr3:50552800-50554400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:50552800-50554400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:50552800-50554400	Enhancers	Adipose Nuclei	Adipose
34	chr3:50552800-50554400	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:50552800-50554400	Bivalent Enhancer	Fetal Thymus	thymus
36	chr3:50552800-50554400	Enhancers	Right Ventricle	heart
37	chr3:50552800-50554400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr3:50552800-50554600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:50552800-50554600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:50552800-50554800	Enhancers	Ovary	ovary
41	chr3:50552800-50555200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:50553000-50553800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:50553000-50553800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:50553000-50553800	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr3:50553000-50553800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:50553000-50553800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:50553000-50553800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr3:50553000-50553800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:50553000-50553800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr3:50553000-50553800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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