Variant report

Variant	rs2904259
Chromosome Location	chr4:89885714-89885715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89879550..89882970-chr4:89885286..89887934,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10008568	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[ASN][1000 genomes]
rs10015415	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs13149750	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs1458562	1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[ASN][1000 genomes]
rs1708667	0.80[ASN][1000 genomes]
rs1795720	0.80[ASN][1000 genomes]
rs1795736	0.80[ASN][1000 genomes]
rs1795739	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1812329	0.95[ASN][1000 genomes]
rs1903003	0.94[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1964516	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2013701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045517	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[ASN][1000 genomes]
rs2125409	0.83[ASN][1000 genomes]
rs2178586	0.80[ASN][1000 genomes]
rs2446300	0.83[CHB][hapmap]
rs2446301	0.82[CHB][hapmap]
rs2609258	0.83[CHB][hapmap]
rs2609259	0.82[CHB][hapmap]
rs2609261	0.83[CHB][hapmap]
rs2609262	0.83[CHB][hapmap]
rs2609279	0.82[CHB][hapmap]
rs2609280	0.83[CHB][hapmap]
rs2704589	0.83[CHB][hapmap]
rs2869966	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[ASN][1000 genomes]
rs2869967	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[ASN][1000 genomes]
rs3846287	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4416442	0.94[ASN][1000 genomes]
rs4505789	0.86[ASN][1000 genomes]
rs4693974	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs4693978	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4693980	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6823536	0.80[ASN][1000 genomes]
rs6824218	0.89[ASN][1000 genomes]
rs6828137	0.84[JPT][hapmap]
rs6837671	0.93[ASN][1000 genomes]
rs6849143	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6852288	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6852928	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7671167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671261	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7674369	0.95[ASN][1000 genomes]
rs7682317	0.94[ASN][1000 genomes]
rs7690839	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv879533	chr4:89832532-89917135	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv1829430	chr4:89853598-89908308	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89871000-89888600	Weak transcription	Small Intestine	intestine
2	chr4:89873000-89886000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr4:89877000-89889000	Weak transcription	Gastric	stomach
4	chr4:89878400-89927600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:89878600-89888600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:89879600-89885800	Weak transcription	Esophagus	oesophagus
7	chr4:89879600-89888800	Weak transcription	Psoas Muscle	Psoas
8	chr4:89879600-89894000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:89879600-89911200	Weak transcription	K562	blood
10	chr4:89879600-89913000	Weak transcription	Aorta	Aorta
11	chr4:89879800-89894600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:89879800-89909200	Weak transcription	Ovary	ovary
13	chr4:89880000-89902400	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:89880000-89903000	Weak transcription	Pancreas	Pancrea
15	chr4:89882200-89889000	Weak transcription	Hela-S3	cervix
16	chr4:89882400-89885800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:89882400-89889000	Weak transcription	Adipose Nuclei	Adipose
18	chr4:89882400-89894200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:89882400-89916400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:89883400-89886400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:89883600-89886600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:89884000-89886400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:89884200-89887000	Enhancers	Placenta	Placenta
24	chr4:89884600-89886400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:89884600-89886600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:89884600-89886600	Enhancers	Stomach Mucosa	stomach
27	chr4:89884600-89886600	Enhancers	HMEC	breast
28	chr4:89884600-89886600	Enhancers	NHDF-Ad	bronchial
29	chr4:89884800-89886400	Enhancers	NHEK	skin
30	chr4:89884800-89886600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr4:89885000-89886000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:89885000-89886000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:89885200-89889000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:89885400-89885800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr4:89885400-89886200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:89885400-89886400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:89885400-89886400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:89885400-89886800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:89885400-89887000	Weak transcription	Fetal Intestine Large	intestine
40	chr4:89885400-89888400	Weak transcription	A549	lung
41	chr4:89885600-89886000	Weak transcription	NHLF	lung
42	chr4:89885600-89886200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:89885600-89887400	Weak transcription	Fetal Intestine Small	intestine
44	chr4:89885600-89889200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:89885600-89894600	Weak transcription	Fetal Lung	lung

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