Variant report

Variant	rs36054388
Chromosome Location	chr1:223003059-223003060
allele	C/T
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	TCF12	chr1:223002983-223003681	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr1:223002976-223003806	SK-N-SH	brain:	n/a	n/a
3	EP300	chr1:223003012-223003806	SK-N-SH	brain:	n/a	chr1:223003616-223003630
4	CTCF	chr1:223003011-223003080	GM20000	blood:	n/a	n/a
5	GATA3	chr1:223002967-223003825	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:222998480..223000211-chr1:223000918..223003363,2	MCF-7	breast:
2	chr1:223001258..223003363-chr1:223007467..223009599,2	MCF-7	breast:
3	chr1:222986729..222989819-chr1:223001002..223005734,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228106	TF binding region
ENSG00000154309	Chromatin interaction
ENSG00000228106	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11485186	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11486081	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163517	0.84[ASN][1000 genomes]
rs34331188	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35264472	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35970216	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71644707	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr1:222989400-223026800	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:222990400-223027400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:222991200-223010200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:222991800-223003200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:222991800-223017200	Weak transcription	Aorta	Aorta
6	chr1:222994000-223003200	Weak transcription	Osteobl	bone
7	chr1:222994600-223003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:222994800-223003200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:222995200-223003400	Weak transcription	NHDF-Ad	bronchial
10	chr1:222995800-223003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:222997000-223016600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:222998200-223003200	Weak transcription	A549	lung
13	chr1:222998200-223003600	Weak transcription	Ovary	ovary
14	chr1:222998400-223006600	Weak transcription	Fetal Lung	lung
15	chr1:222998600-223003400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:222999400-223003200	Weak transcription	Stomach Mucosa	stomach
17	chr1:222999600-223015600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:223001200-223003400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:223001400-223003400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr1:223001800-223003800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr1:223001800-223004000	Enhancers	Colon Smooth Muscle	Colon
22	chr1:223001800-223012000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:223001800-223012200	Weak transcription	Hela-S3	cervix
24	chr1:223002200-223017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:223002400-223004000	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:223002600-223003600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:223002600-223003800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:223002600-223003800	Enhancers	HepG2	liver
29	chr1:223002600-223019800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:223002800-223003400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:223002800-223003800	Enhancers	Brain Substantia Nigra	brain
32	chr1:223002800-223004000	Enhancers	Fetal Intestine Large	intestine
33	chr1:223003000-223003400	Weak transcription	Fetal Intestine Small	intestine
34	chr1:223003000-223003800	Weak transcription	Pancreas	Pancrea
35	chr1:223003000-223004200	Weak transcription	Right Atrium	heart

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