Variant report

Variant	rs11940889
Chromosome Location	chr4:55152583-55152584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10003055	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10004857	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010509	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021728	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028020	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10032688	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11133317	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733839	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935157	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13147194	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547905	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2228230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276948	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412556	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412557	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412558	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28374326	0.91[AMR][1000 genomes]
rs28811736	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3690	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733540	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4289498	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864872	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864875	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864876	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732997	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55784333	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60218083	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677708	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9993187	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1004408	chr4:55124471-55179212	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv537099	chr4:55124471-55179212	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1001094	chr4:55131860-55189739	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55121000-55153200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:55137400-55161600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:55139000-55153000	Weak transcription	Fetal Kidney	kidney
4	chr4:55143600-55164600	Weak transcription	Colonic Mucosa	Colon
5	chr4:55145600-55163200	Weak transcription	Gastric	stomach
6	chr4:55147600-55156000	Weak transcription	Right Ventricle	heart
7	chr4:55148200-55166000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:55148200-55167200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:55148400-55153200	Weak transcription	Fetal Heart	heart
10	chr4:55148400-55156000	Weak transcription	Adipose Nuclei	Adipose
11	chr4:55148400-55163800	Strong transcription	Ovary	ovary
12	chr4:55148600-55158000	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:55148600-55162600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:55148600-55163800	Strong transcription	NHLF	lung
15	chr4:55148600-55166400	Strong transcription	Osteobl	bone
16	chr4:55148800-55161400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:55148800-55162600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:55149400-55162600	Weak transcription	Psoas Muscle	Psoas
19	chr4:55149400-55166400	Strong transcription	NHDF-Ad	bronchial
20	chr4:55149600-55162800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:55149800-55153000	Weak transcription	Placenta	Placenta
22	chr4:55149800-55160800	Weak transcription	Pancreas	Pancrea
23	chr4:55149800-55164000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:55150000-55166000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:55150200-55154400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:55150200-55160800	Strong transcription	Fetal Stomach	stomach
27	chr4:55150200-55163600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:55150200-55164000	Strong transcription	Fetal Lung	lung
29	chr4:55150200-55165200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:55150200-55166200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:55150400-55153800	Weak transcription	Fetal Intestine Small	intestine
32	chr4:55150400-55157000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:55150400-55159200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:55150400-55162400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:55150400-55165400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:55150400-55165600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr4:55150800-55154800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:55150800-55157400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:55150800-55157600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:55151000-55153600	Weak transcription	Spleen	Spleen
41	chr4:55151000-55156200	Weak transcription	Fetal Brain Male	brain
42	chr4:55151200-55161800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr4:55151200-55164400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:55151400-55155600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:55151400-55157600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:55151400-55158800	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:55151600-55157200	Strong transcription	NH-A	brain
48	chr4:55151600-55161600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:55151800-55153400	Strong transcription	Aorta	Aorta
50	chr4:55151800-55159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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