Variant report

Variant	rs10024088
Chromosome Location	chr4:47451896-47451897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47386562..47388237-chr4:47450427..47451934,2	K562	blood:
2	chr4:47447345..47449625-chr4:47449993..47452895,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10010080	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10012665	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10013564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10016116	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10016711	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017635	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10020234	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10020578	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10023931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10025348	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028747	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032089	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28401446	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28419082	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28420192	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28437469	0.96[AFR][1000 genomes]
rs28463624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28589311	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28657923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28687404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4408937	0.95[AFR][1000 genomes]
rs55734368	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56318530	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57637672	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57663033	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs58111381	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs58467459	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs58773051	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60201780	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60226159	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60707722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60744249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60950802	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60981397	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs61111807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812797	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6849185	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73813534	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73813544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7656397	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7660975	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7664395	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7664827	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7665847	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7669793	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7681754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7682167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7686306	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7695644	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9990574	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9995173	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998398	0.84[YRI][hapmap]

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	nsv998919	chr4:47207023-47476876	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv879005	chr4:47408838-47548254	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47436800-47465000	Weak transcription	Gastric	stomach
2	chr4:47438600-47464200	Weak transcription	Small Intestine	intestine
3	chr4:47441000-47456000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:47442200-47464000	Weak transcription	Left Ventricle	heart
5	chr4:47443600-47464000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:47444000-47453600	Weak transcription	HSMMtube	muscle
7	chr4:47445000-47454800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:47445200-47453600	Weak transcription	NHDF-Ad	bronchial
9	chr4:47445200-47454600	Weak transcription	Fetal Intestine Small	intestine
10	chr4:47445400-47453600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:47445400-47465000	Weak transcription	Lung	lung
12	chr4:47445600-47452000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:47445600-47453400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:47445600-47453600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:47445600-47454600	Weak transcription	Ovary	ovary
16	chr4:47445600-47464000	Weak transcription	Pancreas	Pancrea
17	chr4:47445600-47464200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:47445600-47464200	Weak transcription	Thymus	Thymus
19	chr4:47445800-47465000	Weak transcription	Aorta	Aorta
20	chr4:47446000-47465000	Weak transcription	Esophagus	oesophagus
21	chr4:47446200-47452000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:47446200-47453600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr4:47446200-47453600	Weak transcription	GM12878-XiMat	blood
24	chr4:47446600-47463000	Weak transcription	Brain Anterior Caudate	brain
25	chr4:47446800-47452000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:47447000-47453400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:47447000-47453600	Weak transcription	Fetal Thymus	thymus
28	chr4:47447000-47461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:47447200-47452000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:47447200-47453600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:47447200-47453800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:47447600-47452000	Weak transcription	Primary B cells from cord blood	blood
33	chr4:47448000-47452000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:47449000-47452400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:47449200-47452200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:47449200-47455000	Weak transcription	Fetal Brain Female	brain
37	chr4:47449600-47452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr4:47449600-47464200	Weak transcription	Fetal Brain Male	brain
39	chr4:47449800-47452200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:47449800-47452600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:47449800-47465000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr4:47450000-47454800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:47450200-47452000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:47450200-47452000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:47450200-47452000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:47450200-47452000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:47450200-47453600	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:47450400-47452000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:47450400-47452000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:47450400-47452000	Weak transcription	Placenta	Placenta

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