Variant report

Variant	rs60478034
Chromosome Location	chr5:52240091-52240092
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	chr5:52239227..52240957-chr5:52240958..52243466,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10073432	0.88[AFR][1000 genomes]
rs10940281	0.86[AFR][1000 genomes]
rs1363189	0.87[AFR][1000 genomes]
rs1421927	0.88[AFR][1000 genomes]
rs1421928	0.87[AFR][1000 genomes]
rs2406371	0.87[AFR][1000 genomes]
rs6888620	0.90[AFR][1000 genomes]
rs7702592	0.85[AFR][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	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 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	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52206400-52240800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:52211400-52240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:52211600-52244400	Weak transcription	HepG2	liver
5	chr5:52218600-52242200	Weak transcription	Fetal Kidney	kidney
6	chr5:52218800-52240800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:52219200-52240800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:52219200-52240800	Weak transcription	NHLF	lung
9	chr5:52220000-52243000	Weak transcription	Gastric	stomach
10	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:52221400-52240600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:52224200-52244600	Weak transcription	Primary T cells from cord blood	blood
14	chr5:52227000-52240800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:52228400-52240800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:52231600-52245400	Weak transcription	Colonic Mucosa	Colon
18	chr5:52232200-52240600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
20	chr5:52235000-52240800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:52235400-52243200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:52236000-52240400	Weak transcription	NHDF-Ad	bronchial
23	chr5:52236000-52240800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:52237000-52240800	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:52237400-52240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:52237400-52240800	Weak transcription	Adipose Nuclei	Adipose
27	chr5:52238800-52240200	Strong transcription	Fetal Lung	lung
28	chr5:52238800-52252200	Strong transcription	Liver	Liver
29	chr5:52239000-52240400	Strong transcription	Fetal Intestine Large	intestine
30	chr5:52239200-52240200	Genic enhancers	Spleen	Spleen
31	chr5:52239400-52240200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:52239400-52240200	Strong transcription	Fetal Intestine Small	intestine
33	chr5:52239400-52240200	Strong transcription	Fetal Muscle Leg	muscle
34	chr5:52239400-52240200	Strong transcription	Fetal Stomach	stomach
35	chr5:52239600-52240800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:52239800-52240400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:52239800-52240800	Weak transcription	Right Atrium	heart
38	chr5:52240000-52240400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
39	chr5:52240000-52240800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:52240000-52240800	Enhancers	Dnd41	blood
41	chr5:52240000-52245400	Weak transcription	Placenta	Placenta
42	chr5:52240000-52249800	Weak transcription	Aorta	Aorta
43	chr5:52240000-52253000	Weak transcription	Right Ventricle	heart
44	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
45	chr5:52240000-52253600	Weak transcription	Lung	lung

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