Variant report

Variant	rs28708409
Chromosome Location	chr2:47296806-47296807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47292753..47295040-chr2:47295086..47296982,3	MCF-7	breast:
2	chr2:47295023..47298657-chr2:47300855..47310213,9	MCF-7	breast:
3	chr2:47295441..47298329-chr2:47298635..47300784,3	MCF-7	breast:
4	chr2:47271650..47273427-chr2:47295265..47298001,2	MCF-7	breast:
5	chr2:47295079..47297888-chr2:47402697..47404498,3	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000225187	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10174635	0.91[AMR][1000 genomes]
rs10191558	0.91[AMR][1000 genomes]
rs17036191	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs60472761	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs61089798	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6708855	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6733891	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6749079	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs919878	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs919879	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 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	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47284600-47298400	Strong transcription	Thymus	Thymus
3	chr2:47288000-47300400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:47290400-47299000	Genic enhancers	Fetal Muscle Leg	muscle
5	chr2:47290800-47297800	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:47291600-47300800	Weak transcription	Brain Germinal Matrix	brain
7	chr2:47291800-47297800	Genic enhancers	Spleen	Spleen
8	chr2:47291800-47301200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr2:47292000-47298800	Enhancers	Placenta	Placenta
10	chr2:47292200-47298200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:47292400-47299600	Enhancers	HUVEC	blood vessel
12	chr2:47292600-47302200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:47292800-47300000	Enhancers	NHDF-Ad	bronchial
14	chr2:47293000-47297400	Weak transcription	Fetal Kidney	kidney
15	chr2:47293000-47300600	Enhancers	Right Ventricle	heart
16	chr2:47293000-47301400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr2:47293200-47299200	Enhancers	Liver	Liver
18	chr2:47293400-47297400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:47294200-47298000	Enhancers	Pancreas	Pancrea
20	chr2:47294200-47298200	Genic enhancers	NHLF	lung
21	chr2:47294400-47298600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:47294400-47301000	Enhancers	Right Atrium	heart
23	chr2:47294600-47300000	Enhancers	Brain Substantia Nigra	brain
24	chr2:47294800-47297400	Enhancers	HSMMtube	muscle
25	chr2:47294800-47297800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr2:47295000-47299200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:47295000-47299200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:47295000-47299200	Enhancers	Psoas Muscle	Psoas
29	chr2:47295000-47299200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr2:47295000-47300000	Enhancers	Fetal Muscle Trunk	muscle
31	chr2:47295000-47300600	Enhancers	Primary hematopoietic stem cells	blood
32	chr2:47295000-47300600	Genic enhancers	Fetal Stomach	stomach
33	chr2:47295000-47300600	Enhancers	Ovary	ovary
34	chr2:47295000-47300600	Enhancers	NH-A	brain
35	chr2:47295000-47301200	Enhancers	Left Ventricle	heart
36	chr2:47295000-47301400	Genic enhancers	Esophagus	oesophagus
37	chr2:47295200-47297200	Enhancers	Brain Anterior Caudate	brain
38	chr2:47295200-47297400	Enhancers	Osteobl	bone
39	chr2:47295200-47298800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr2:47295200-47299200	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:47295400-47297800	Enhancers	Hela-S3	cervix
42	chr2:47295400-47298000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr2:47295400-47298400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr2:47295400-47298400	Enhancers	Brain Hippocampus Middle	brain
45	chr2:47295400-47298800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:47295400-47299000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:47295400-47299200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:47295400-47299600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:47295400-47300200	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr2:47295400-47301000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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