Variant report

Variant	rs28385616
Chromosome Location	chr6:12957480-12957481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:12957402-12957869	HUVEC	blood vessel:	n/a	n/a
2	MXI1	chr6:12957266-12959118	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:12957477-12958503	HUVEC	blood vessel:	n/a	n/a
4	BACH1	chr6:12957431-12957748	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF384	chr6:12957420-12957653	GM12878	blood:	n/a	n/a
6	USF1	chr6:12957293-12957512	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr6:12957336-12958348	NB4	blood:	n/a	chr6:12958035-12958050

Variant related genes	Relation type
PHACTR1	TF binding region

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

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

rs_ID	r²[population]
rs13211739	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34054869	0.84[AMR][1000 genomes]
rs34476983	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34541307	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35056688	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36100854	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67061558	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67193572	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72820839	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72820847	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv5202	chr6:12916229-12958517	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12955800-12958800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:12956400-12957800	Active TSS	Primary hematopoietic stem cells	blood
3	chr6:12956600-12958400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr6:12956600-12958400	Active TSS	Primary T cells from cord blood	blood
5	chr6:12956800-12957600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:12956800-12958000	Active TSS	Primary B cells from cord blood	blood
7	chr6:12956800-12959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:12957000-12957600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
9	chr6:12957000-12957600	Active TSS	Adipose Nuclei	Adipose
10	chr6:12957000-12957800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
11	chr6:12957000-12957800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:12957000-12957800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:12957000-12957800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:12957000-12958000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:12957000-12958000	Active TSS	Duodenum Mucosa	Duodenum
16	chr6:12957000-12958200	Flanking Bivalent TSS/Enh	Dnd41	blood
17	chr6:12957000-12958400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:12957000-12959000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:12957000-12959000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:12957000-12959000	Active TSS	HSMMtube	muscle
21	chr6:12957000-12959000	Active TSS	NHDF-Ad	bronchial
22	chr6:12957000-12959200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:12957000-12959400	Active TSS	Brain Hippocampus Middle	brain
24	chr6:12957000-12960000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:12957200-12957600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:12957200-12957600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr6:12957200-12957600	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr6:12957200-12957800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr6:12957200-12957800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:12957200-12957800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
31	chr6:12957200-12957800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
32	chr6:12957200-12958000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
33	chr6:12957200-12958000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr6:12957200-12958000	Active TSS	Primary monocytes fromperipheralblood	blood
35	chr6:12957200-12958000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:12957200-12958000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:12957200-12958200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr6:12957200-12958200	Active TSS	Fetal Lung	lung
39	chr6:12957200-12958200	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:12957200-12958400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr6:12957200-12958400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:12957200-12958400	Active TSS	Psoas Muscle	Psoas
43	chr6:12957200-12958400	Active TSS	Small Intestine	intestine
44	chr6:12957200-12958800	Active TSS	Brain Anterior Caudate	brain
45	chr6:12957200-12958800	Active TSS	Ovary	ovary
46	chr6:12957200-12958800	Active TSS	Thymus	Thymus
47	chr6:12957200-12959000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:12957200-12959000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:12957200-12959000	Active TSS	Brain Cingulate Gyrus	brain
50	chr6:12957200-12959200	Active TSS	Primary hematopoietic stem cells short term culture	blood

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