Variant report

Variant	rs2758875
Chromosome Location	chr6:39247671-39247672
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39236174..39238959-chr6:39247299..39249650,2	MCF-7	breast:
2	chr6:39246289..39249933-chr6:39249942..39252765,4	MCF-7	breast:
3	chr6:39135484..39137595-chr6:39246692..39248573,2	MCF-7	breast:
4	chr6:39243650..39250520-chr6:39262135..39271800,15	MCF-7	breast:
5	chr6:39246522..39249278-chr6:39249658..39251560,2	MCF-7	breast:
6	chr6:39242418..39244408-chr6:39246030..39248375,3	MCF-7	breast:
7	chr6:39245951..39248389-chr6:39255673..39257874,2	MCF-7	breast:
8	chr6:39245598..39248423-chr6:39251437..39253909,2	K562	blood:
9	chr6:39195286..39197963-chr6:39246502..39249488,3	K562	blood:
10	chr6:39191982..39197381-chr6:39245126..39249052,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12194951	0.93[ASN][1000 genomes]
rs12197500	0.87[ASN][1000 genomes]
rs12201021	0.84[ASN][1000 genomes]
rs12214300	0.84[ASN][1000 genomes]
rs12214342	0.84[ASN][1000 genomes]
rs16891847	0.87[ASN][1000 genomes]
rs16891848	0.87[ASN][1000 genomes]
rs2758862	0.84[ASN][1000 genomes]
rs2815022	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34625110	0.84[ASN][1000 genomes]
rs6940480	0.95[ASN][1000 genomes]
rs9349112	0.91[ASN][1000 genomes]
rs9349113	0.91[ASN][1000 genomes]
rs9367000	0.90[ASN][1000 genomes]
rs9367001	0.89[ASN][1000 genomes]
rs9367002	0.90[ASN][1000 genomes]
rs9369111	0.91[ASN][1000 genomes]
rs9380846	0.90[ASN][1000 genomes]
rs9394581	0.91[ASN][1000 genomes]
rs9394582	0.91[ASN][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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39240400-39250200	Enhancers	Stomach Mucosa	stomach
2	chr6:39242000-39247800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:39242600-39249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:39245800-39248600	Enhancers	Placenta	Placenta
5	chr6:39246200-39251000	Enhancers	Liver	Liver
6	chr6:39246800-39248600	Enhancers	Small Intestine	intestine
7	chr6:39246800-39250400	Enhancers	Esophagus	oesophagus
8	chr6:39247000-39249000	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:39247000-39250200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:39247000-39250200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr6:39247000-39250400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:39247200-39248600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:39247200-39249000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:39247200-39250400	Enhancers	Colonic Mucosa	Colon
15	chr6:39247400-39247800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr6:39247400-39248200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:39247400-39248400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:39247400-39248400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:39247400-39249200	Enhancers	Lung	lung
20	chr6:39247600-39247800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:39247600-39248000	Enhancers	Hela-S3	cervix
22	chr6:39247600-39248200	Enhancers	Fetal Thymus	thymus
23	chr6:39247600-39248400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:39247600-39248400	Enhancers	Pancreas	Pancrea
25	chr6:39247600-39248600	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr6:39247600-39248800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:39247600-39249200	Weak transcription	Gastric	stomach

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