Variant report

Variant	rs28780098
Chromosome Location	chr6:30303368-30303369
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30298070..30301347-chr6:30302009..30303774,3	MCF-7	breast:
2	chr6:30300818..30303385-chr6:30311181..30313582,3	MCF-7	breast:
3	chr6:30301782..30303711-chr6:30308127..30310894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241370	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17475879	1.00[AMR][1000 genomes]
rs28780088	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780089	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780090	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780092	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780107	0.83[AMR][1000 genomes]
rs28780108	0.91[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30295400-30303400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:30295400-30309400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:30295600-30303400	Weak transcription	Psoas Muscle	Psoas
4	chr6:30295600-30312600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:30295600-30312600	Weak transcription	Right Atrium	heart
6	chr6:30295600-30313000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:30295800-30303400	Weak transcription	A549	lung
8	chr6:30295800-30311000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:30295800-30312400	Weak transcription	Fetal Heart	heart
10	chr6:30295800-30312400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:30296200-30310400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:30296600-30310600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr6:30296800-30310000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:30296800-30310000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:30296800-30310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:30296800-30310400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr6:30296800-30310600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:30296800-30310800	Strong transcription	Fetal Brain Female	brain
19	chr6:30296800-30311200	Strong transcription	Placenta	Placenta
20	chr6:30296800-30311400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:30296800-30311800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:30297000-30304200	Strong transcription	Ovary	ovary
23	chr6:30297000-30305000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:30297000-30306000	Strong transcription	HSMM	muscle
25	chr6:30297000-30306200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr6:30297000-30307800	Strong transcription	Osteobl	bone
27	chr6:30297000-30310000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:30297000-30310200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:30297000-30310200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr6:30297000-30310400	Strong transcription	Brain Cingulate Gyrus	brain
31	chr6:30297000-30310600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:30297000-30311000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:30297200-30304600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr6:30297200-30305800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:30297200-30306000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:30297200-30310200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:30297200-30310200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:30297200-30310200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:30297200-30310200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr6:30297200-30310200	Strong transcription	NHEK	skin
41	chr6:30297200-30310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:30297200-30310400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr6:30297200-30310400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:30297200-30310600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:30297200-30310600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:30297200-30310800	Strong transcription	Liver	Liver
47	chr6:30297200-30310800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:30297200-30310800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:30297200-30311000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:30297200-30311000	Strong transcription	Adipose Nuclei	Adipose

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