Variant report

Variant	rs6840039
Chromosome Location	chr4:148687334-148687335
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:148682718..148685526-chr4:148687157..148689131,2	K562	blood:
2	chr4:148652539..148655321-chr4:148686401..148688051,2	MCF-7	breast:
3	chr4:148681549..148683602-chr4:148686887..148689104,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10027921	0.80[AMR][1000 genomes]
rs11099669	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11729081	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12640660	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12645249	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12648074	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12650280	0.80[AMR][1000 genomes]
rs13116955	0.80[AMR][1000 genomes]
rs13134018	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13136624	0.82[AFR][1000 genomes]
rs2055551	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2134706	0.80[AMR][1000 genomes]
rs2164527	0.88[AFR][1000 genomes]
rs62330668	0.88[AMR][1000 genomes]
rs6535558	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6535559	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6535560	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6535561	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6822971	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6839987	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6845560	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7673234	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7673606	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9332471	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs964170	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]

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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880242	chr4:148659137-148727355	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148663600-148688800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:148670200-148693200	Weak transcription	Esophagus	oesophagus
3	chr4:148677600-148689000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:148677800-148688800	Weak transcription	NH-A	brain
5	chr4:148678000-148689000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:148678000-148689200	Weak transcription	HSMMtube	muscle
7	chr4:148678000-148693200	Weak transcription	Adipose Nuclei	Adipose
8	chr4:148678200-148688800	Weak transcription	Osteobl	bone
9	chr4:148679200-148689200	Weak transcription	Gastric	stomach
10	chr4:148679200-148689200	Weak transcription	NHLF	lung
11	chr4:148679200-148693000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:148679200-148693000	Weak transcription	Aorta	Aorta
13	chr4:148679200-148696400	Weak transcription	Lung	lung
14	chr4:148682000-148688800	Weak transcription	Fetal Intestine Small	intestine
15	chr4:148682000-148689000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:148682000-148689000	Weak transcription	A549	lung
17	chr4:148682200-148688800	Weak transcription	HSMM	muscle
18	chr4:148682200-148693000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:148682400-148692400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:148682800-148689000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:148683000-148689200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:148683000-148689200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:148683200-148688800	Weak transcription	GM12878-XiMat	blood
24	chr4:148683400-148689200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:148683600-148688800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:148683600-148688800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:148684000-148688200	Weak transcription	Left Ventricle	heart
28	chr4:148684200-148691800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:148684400-148693600	Weak transcription	Fetal Kidney	kidney
30	chr4:148685200-148692200	Weak transcription	Right Atrium	heart
31	chr4:148685600-148688800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:148685600-148691200	Weak transcription	Psoas Muscle	Psoas
33	chr4:148685800-148688800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:148686000-148688800	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:148686000-148693000	Weak transcription	Ovary	ovary
36	chr4:148686200-148687600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:148686200-148689200	Weak transcription	Fetal Heart	heart
38	chr4:148686400-148687400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:148686400-148688800	Weak transcription	NHDF-Ad	bronchial
40	chr4:148686600-148688800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:148686800-148688600	Weak transcription	Pancreas	Pancrea
42	chr4:148687000-148687400	Strong transcription	Fetal Muscle Leg	muscle
43	chr4:148687000-148688200	Weak transcription	Stomach Mucosa	stomach
44	chr4:148687000-148688800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:148687000-148692000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:148687200-148688800	Weak transcription	HMEC	breast
47	chr4:148687200-148689000	Weak transcription	NHEK	skin
48	chr4:148687200-148689200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:148687200-148696400	Weak transcription	Right Ventricle	heart

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