Variant report

Variant	rs3800317
Chromosome Location	chr6:27258972-27258973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27258318..27260398-chr6:27469283..27471523,2	K562	blood:
2	chr6:27258451..27260109-chr6:27301059..27302632,2	K562	blood:
3	chr6:27203282..27204812-chr6:27256715..27259261,2	K562	blood:
4	chr6:27258123..27260982-chr6:27774504..27777198,2	K562	blood:
5	chr6:27258656..27261261-chr6:27270962..27272747,2	K562	blood:
6	chr6:27102356..27104874-chr6:27257312..27259023,2	K562	blood:
7	chr6:27257414..27260339-chr6:27439402..27443718,5	K562	blood:
8	chr6:27201566..27203350-chr6:27258009..27260418,2	K562	blood:
9	chr6:27144021..27146883-chr6:27258754..27261461,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000185130	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13437532	1.00[CEU][hapmap]
rs16897345	0.89[CHB][hapmap];0.93[EUR][1000 genomes]
rs16897467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16897557	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2393918	1.00[CEU][hapmap]
rs41473150	1.00[CEU][hapmap]
rs4582379	1.00[CEU][hapmap]
rs4711143	1.00[CEU][hapmap]
rs61249083	0.93[EUR][1000 genomes]
rs6922098	1.00[CEU][hapmap]
rs73390697	0.93[EUR][1000 genomes]
rs9366683	1.00[CEU][hapmap]
rs9468060	1.00[CEU][hapmap];0.80[EUR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27257800-27259000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27257800-27259000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr6:27257800-27259000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:27257800-27259200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:27257800-27259200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:27257800-27259200	Active TSS	NHEK	skin
7	chr6:27257800-27259400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:27257800-27259400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr6:27257800-27259400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:27257800-27259600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:27257800-27260000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:27258000-27259000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:27258000-27259000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:27258000-27259200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:27258000-27259600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:27258000-27260000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:27258000-27261800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr6:27258200-27259200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:27258200-27259200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:27258200-27259200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:27258200-27259200	Bivalent/Poised TSS	Osteobl	bone
22	chr6:27258400-27259000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:27258400-27259000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:27258400-27259000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:27258400-27259000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr6:27258400-27261200	Weak transcription	HMEC	breast
27	chr6:27258600-27259000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:27258600-27259000	Bivalent Enhancer	HepG2	liver
29	chr6:27258600-27259200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:27258600-27259200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
31	chr6:27258600-27259200	Flanking Active TSS	K562	blood
32	chr6:27258600-27259400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:27258800-27259000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:27258800-27259000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:27258800-27261000	Weak transcription	A549	lung

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