Variant report

Variant	rs28519621
Chromosome Location	chr4:90043116-90043117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90031396..90034227-chr4:90041663..90045608,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-4	chr4:90042215-90044000	NONHSAT097383

Variant related genes	Relation type
ENSG00000271359	Chromatin interaction
ENSG00000138640	Chromatin interaction
ENSG00000180346	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10028786	1.00[AMR][1000 genomes]
rs28484695	0.93[AMR][1000 genomes]
rs28521479	0.93[AMR][1000 genomes]
rs28575566	1.00[AMR][1000 genomes]
rs28657568	0.93[AMR][1000 genomes]
rs28875200	0.83[AMR][1000 genomes]
rs6816195	1.00[AMR][1000 genomes]
rs6816472	0.93[AMR][1000 genomes]
rs6818212	0.93[AMR][1000 genomes]
rs6818976	0.93[AMR][1000 genomes]
rs6845151	0.93[AMR][1000 genomes]
rs7666393	0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
5	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
6	chr4:90033600-90049200	Weak transcription	Gastric	stomach
7	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
8	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:90035600-90043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:90035600-90044000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:90036600-90044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:90037000-90046200	Weak transcription	Primary T cells from cord blood	blood
18	chr4:90039200-90044600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:90039800-90043400	Weak transcription	Placenta	Placenta
20	chr4:90039800-90043800	Weak transcription	Liver	Liver
21	chr4:90041000-90043200	Weak transcription	HMEC	breast
22	chr4:90041200-90043200	Weak transcription	NHEK	skin
23	chr4:90041400-90043800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:90041600-90044000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:90041600-90044000	Weak transcription	NH-A	brain
26	chr4:90041600-90045200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:90042200-90047600	Enhancers	Fetal Intestine Large	intestine
28	chr4:90042400-90044800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:90042600-90043400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:90042600-90044200	Enhancers	K562	blood
31	chr4:90042600-90049600	Enhancers	Fetal Intestine Small	intestine
32	chr4:90042800-90043200	Flanking Active TSS	A549	lung
33	chr4:90042800-90043600	Enhancers	HepG2	liver
34	chr4:90043000-90043200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr4:90043000-90043200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:90043000-90043200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:90043000-90043200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr4:90043000-90043800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:90043000-90045200	Enhancers	Stomach Mucosa	stomach

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