Variant report

Variant	rs10027975
Chromosome Location	chr4:54054763-54054764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11133248	0.80[EUR][1000 genomes]
rs11721940	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11942132	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12715997	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13146499	0.83[EUR][1000 genomes]
rs2412403	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412404	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34426398	0.85[AFR][1000 genomes]
rs4394057	0.86[EUR][1000 genomes]
rs4588514	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4864737	0.80[EUR][1000 genomes]
rs6554071	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554074	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554075	0.81[EUR][1000 genomes]
rs6554078	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6822933	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6827392	0.83[EUR][1000 genomes]
rs7655632	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7672997	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7673864	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7687452	0.87[EUR][1000 genomes]
rs9990771	0.81[AFR][1000 genomes]
rs9991945	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54038800-54054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:54043200-54077000	Weak transcription	Primary T cells from cord blood	blood
3	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
4	chr4:54050200-54061800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:54050400-54062400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:54051000-54073000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:54052000-54055400	Enhancers	Fetal Intestine Large	intestine
8	chr4:54052000-54055800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:54052000-54056600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:54052200-54055800	Enhancers	HepG2	liver
11	chr4:54052200-54056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:54052200-54056600	Enhancers	NHDF-Ad	bronchial
13	chr4:54052400-54056000	Enhancers	NH-A	brain
14	chr4:54052400-54065800	Weak transcription	Aorta	Aorta
15	chr4:54052800-54056600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:54053000-54093000	Weak transcription	Primary B cells from cord blood	blood
17	chr4:54053200-54058000	Weak transcription	Small Intestine	intestine
18	chr4:54053600-54055400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr4:54053600-54055800	Enhancers	NHLF	lung
20	chr4:54053800-54055400	Enhancers	Fetal Lung	lung
21	chr4:54053800-54055800	Enhancers	HSMM	muscle
22	chr4:54054000-54056600	Enhancers	HSMMtube	muscle
23	chr4:54054200-54054800	Flanking Active TSS	Liver	Liver
24	chr4:54054200-54054800	Enhancers	Duodenum Mucosa	Duodenum
25	chr4:54054200-54054800	Flanking Active TSS	A549	lung
26	chr4:54054200-54055000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:54054400-54054800	Enhancers	Fetal Brain Male	brain
28	chr4:54054400-54054800	Enhancers	Fetal Stomach	stomach
29	chr4:54054400-54055000	Weak transcription	Fetal Intestine Small	intestine
30	chr4:54054400-54055000	Weak transcription	Fetal Kidney	kidney
31	chr4:54054400-54055200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:54054400-54055200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:54054400-54055200	Flanking Active TSS	Osteobl	bone
34	chr4:54054400-54056000	Enhancers	Ovary	ovary
35	chr4:54054600-54054800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:54054600-54054800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr4:54054600-54055000	Enhancers	Stomach Mucosa	stomach
38	chr4:54054600-54056000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:54054600-54072200	Weak transcription	K562	blood

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