Variant report

Variant	rs72968358
Chromosome Location	chr1:95008555-95008556
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	POLR2A	chr1:95008440-95008903	U87	brain:	n/a	n/a
2	GTF2F1	chr1:95007247-95008830	Hela-S3	cervix:	n/a	n/a
3	MYC	chr1:95008320-95008915	MCF10A-Er-Src	breast:	n/a	chr1:95008768-95008777
4	STAT3	chr1:95008500-95008860	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr1:95008480-95008630	NHLF	lung:	n/a	n/a
6	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
7	POLR2A	chr1:95008543-95008884	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:95008484-95008958	HUVEC	blood vessel:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777
10	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a
11	SPI1	chr1:95008550-95008866	HL-60	blood:	n/a	n/a
12	FOS	chr1:95008408-95008967	MCF10A-Er-Src	breast:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777
13	TBP	chr1:95008031-95008941	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr1:95006194-95008967	IMR90	lung:	n/a	chr1:95007044-95007058
15	FOS	chr1:95008276-95008954	MCF10A-Er-Src	breast:	n/a	chr1:95008770-95008777 chr1:95008769-95008777 chr1:95008769-95008777

No.	Distal block	Cell Line	Cell type
1	chr1:95007807..95010747-chr1:95056056..95057592,2	MCF-7	breast:
2	chr1:95001173..95003691-chr1:95006398..95009153,2	MCF-7	breast:
3	chr1:95007807..95010270-chr1:95025313..95026976,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABCD3-1	chr1:95008015-95008571	XLOC_000302
2	lnc-ABCD3-1	chr1:95007516-95008786	NONHSAT004594

Variant related genes	Relation type
F3	TF binding region
ENSG00000117525	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs6691552	1.00[AMR][1000 genomes]
rs72968355	1.00[AMR][1000 genomes]
rs72968359	1.00[AMR][1000 genomes]
rs841342	1.00[AMR][1000 genomes]
rs841350	1.00[AMR][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	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3437143	chr1:95006189-95008737	Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95004200-95008800	Active TSS	Ovary	ovary
2	chr1:95005600-95008800	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:95005800-95008600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:95006200-95008600	Active TSS	Aorta	Aorta
5	chr1:95006600-95008600	Active TSS	NHLF	lung
6	chr1:95006600-95008800	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr1:95006800-95008600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:95006800-95008600	Active TSS	NHEK	skin
9	chr1:95006800-95009200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:95007000-95009400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:95007200-95009600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:95007400-95009400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:95007600-95008600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:95007600-95008600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr1:95007600-95008600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr1:95007600-95008600	Flanking Active TSS	Liver	Liver
17	chr1:95007600-95008600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:95007600-95008600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
19	chr1:95007600-95008800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:95007600-95008800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr1:95007600-95008800	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:95007600-95008800	Flanking Active TSS	Dnd41	blood
23	chr1:95007600-95008800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
24	chr1:95007600-95008800	Flanking Active TSS	Hela-S3	cervix
25	chr1:95007600-95008800	Flanking Active TSS	Osteobl	bone
26	chr1:95007600-95009000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:95007600-95009000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:95007600-95009000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:95007600-95010400	Flanking Active TSS	HMEC	breast
30	chr1:95007800-95008600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
31	chr1:95007800-95008600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
32	chr1:95007800-95008600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr1:95007800-95008800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:95007800-95008800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:95007800-95008800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:95007800-95008800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr1:95007800-95008800	Flanking Active TSS	NH-A	brain
38	chr1:95008000-95008600	Active TSS	Brain Anterior Caudate	brain
39	chr1:95008000-95008600	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr1:95008000-95008600	Enhancers	Small Intestine	intestine
41	chr1:95008000-95008800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
42	chr1:95008000-95008800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:95008000-95008800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
44	chr1:95008000-95008800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
45	chr1:95008000-95008800	Bivalent Enhancer	Fetal Thymus	thymus
46	chr1:95008000-95009000	Flanking Active TSS	A549	lung
47	chr1:95008000-95010600	Enhancers	HSMMtube	muscle
48	chr1:95008200-95008600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:95008200-95008600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
50	chr1:95008200-95008600	Active TSS	Fetal Brain Female	brain

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