Variant report

Variant	rs781228
Chromosome Location	chr1:45877631-45877632
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	GATA3	chr1:45877093-45877659	T-47D	breast:	n/a	n/a
2	GATA3	chr1:45877135-45877651	T-47D	breast:	n/a	n/a
3	CTCF	chr1:45877540-45877690	NHEK	skin:	n/a	n/a
4	GATA3	chr1:45876278-45877696	MCF-7	breast:	n/a	n/a
5	JUN	chr1:45876543-45878303	K562	blood:	n/a	n/a
6	SIN3AK20	chr1:45876416-45877695	MCF-7	breast:	n/a	n/a
7	ZNF217	chr1:45876625-45877696	MCF-7	breast:	n/a	n/a
8	GATA3	chr1:45876576-45877654	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45806484..45809522-chr1:45876686..45880375,3	K562	blood:

Variant related genes	Relation type
ENSG00000236872	TF binding region
ENSG00000132773	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1691220	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59517508	1.00[AMR][1000 genomes]
rs72890555	1.00[AMR][1000 genomes]
rs7519633	0.85[YRI][hapmap]
rs7555357	1.00[AMR][1000 genomes]
rs781227	1.00[AFR][1000 genomes]
rs781229	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9429064	1.00[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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
9	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45841400-45889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45869400-45885400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:45875600-45878600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:45875600-45889400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:45876600-45878400	Enhancers	K562	blood
6	chr1:45876600-45880000	Enhancers	Primary B cells from cord blood	blood
7	chr1:45876600-45880400	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:45876600-45881600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:45876800-45877800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:45876800-45879200	Enhancers	GM12878-XiMat	blood
11	chr1:45876800-45887800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:45877000-45878600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:45877000-45886800	Weak transcription	Liver	Liver
14	chr1:45877200-45877800	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:45877200-45887800	Weak transcription	Fetal Intestine Large	intestine
16	chr1:45877200-45888200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:45877400-45877800	Enhancers	NHEK	skin
18	chr1:45877400-45878200	Enhancers	Hela-S3	cervix
19	chr1:45877400-45886800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:45877400-45889200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:45877600-45878600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:45877600-45878600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:45877600-45878800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:45877600-45887400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:45877600-45889600	Weak transcription	Placenta	Placenta

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