Variant report

Variant	rs41308291
Chromosome Location	chr5:52285909-52285910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:121484544..121485273-chr5:52285389..52286031,2	Hela-S3	cervix:
2	chr5:52285298..52286236-chr8:134310006..134310609,2	Hela-S3	cervix:
3	chr5:52285098..52285959-chr8:128747992..128748939,2	Hela-S3	cervix:
4	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:
5	chr16:70332608..70333198-chr5:52285135..52286085,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000260537	Chromatin interaction
ENSG00000104419	Chromatin interaction
ENSG00000157349	Chromatin interaction
ENSG00000272123	Chromatin interaction
ENSG00000136997	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10038737	0.87[EUR][1000 genomes]
rs10039574	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10052870	0.87[EUR][1000 genomes]
rs13360524	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1421924	0.87[EUR][1000 genomes]
rs16880544	0.87[EUR][1000 genomes]
rs16880552	0.87[EUR][1000 genomes]
rs3733880	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928414	0.88[ASN][1000 genomes]
rs41311329	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52284000-52288000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:52284200-52286400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:52284200-52286600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:52284400-52286200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr5:52284400-52286200	Active TSS	Sigmoid Colon	Sigmoid Colon
6	chr5:52284400-52286400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:52284400-52286400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:52284400-52286400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr5:52284400-52286600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:52284400-52286600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:52284400-52286600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:52284400-52286600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:52284400-52286800	Active TSS	Brain Substantia Nigra	brain
14	chr5:52284400-52287000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr5:52284600-52286000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:52284600-52286000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr5:52284600-52286000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr5:52284600-52286000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:52284600-52286200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:52284600-52286200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:52284600-52286200	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr5:52284600-52286200	Active TSS	Gastric	stomach
23	chr5:52284600-52286200	Active TSS	Ovary	ovary
24	chr5:52284600-52286200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
25	chr5:52284600-52286400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr5:52284600-52286400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr5:52284600-52286400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:52284600-52286400	Bivalent/Poised TSS	HepG2	liver
29	chr5:52284600-52286600	Active TSS	Brain Cingulate Gyrus	brain
30	chr5:52284600-52286600	Active TSS	Esophagus	oesophagus
31	chr5:52284600-52286600	Active TSS	A549	lung
32	chr5:52284600-52286600	Active TSS	NHDF-Ad	bronchial
33	chr5:52284600-52286800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:52284600-52286800	Active TSS	Fetal Brain Female	brain
35	chr5:52284600-52287200	Active TSS	Fetal Kidney	kidney
36	chr5:52284800-52286000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:52284800-52286000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:52284800-52286200	Active TSS	Lung	lung
39	chr5:52284800-52286200	Active TSS	Small Intestine	intestine
40	chr5:52284800-52286200	Active TSS	NH-A	brain
41	chr5:52284800-52286400	Active TSS	Fetal Intestine Small	intestine
42	chr5:52284800-52286400	Active TSS	Osteobl	bone
43	chr5:52284800-52286600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:52284800-52286600	Active TSS	Hela-S3	cervix
45	chr5:52284800-52286800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr5:52284800-52286800	Active TSS	NHEK	skin
47	chr5:52284800-52287200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:52284800-52288200	Active TSS	NHLF	lung
49	chr5:52285000-52286000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
50	chr5:52285000-52286200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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